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Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales." /> <title>(PDF) Models of experimental evolution: the role of genetic chance and selective necessity | David Krakauer - Academia.edu</title> <link rel="canonical" href="https://www.academia.edu/48382628/Models_of_experimental_evolution_the_role_of_genetic_chance_and_selective_necessity" /> <script async src="https://www.googletagmanager.com/gtag/js?id=G-5VKX33P2DS"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-5VKX33P2DS', { cookie_domain: 'academia.edu', send_page_view: false, }); gtag('event', 'page_view', { 'controller': "single_work", 'action': "show", 'controller_action': 'single_work#show', 'logged_in': 'false', 'edge': 'unknown', // Send nil if there is no A/B test bucket, in case some records get logged // with missing data - that way we can distinguish between the two cases. // ab_test_bucket should be of the form <ab_test_name>:<bucket> 'ab_test_bucket': null, }) </script> <script> var $controller_name = 'single_work'; var $action_name = "show"; var $rails_env = 'production'; var $app_rev = '48654d67e5106e06fb1e5c9a356c302510d6cfee'; var $domain = 'academia.edu'; var $app_host = "academia.edu"; var $asset_host = "academia-assets.com"; var $start_time = new Date().getTime(); var $recaptcha_key = "6LdxlRMTAAAAADnu_zyLhLg0YF9uACwz78shpjJB"; var $recaptcha_invisible_key = "6Lf3KHUUAAAAACggoMpmGJdQDtiyrjVlvGJ6BbAj"; var $disableClientRecordHit = false; </script> <script> window.require = { config: function() { return function() {} } } </script> <script> window.Aedu = window.Aedu || {}; window.Aedu.hit_data = null; window.Aedu.serverRenderTime = new Date(1734506090000); window.Aedu.timeDifference = new Date().getTime() - 1734506090000; </script> <script type="application/ld+json">{"@context":"https://schema.org","@type":"ScholarlyArticle","abstract":"We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness inc...","author":[{"@context":"https://schema.org","@type":"Person","name":"David Krakauer"}],"contributor":[],"dateCreated":"2021-05-04","dateModified":"2021-05-04","datePublished":"2000-01-01","headline":"Models of experimental evolution: the role of genetic chance and selective necessity","image":"https://attachments.academia-assets.com/67024372/thumbnails/1.jpg","inLanguage":"en","keywords":[],"publication":"Genetics","publisher":{"@context":"https://schema.org","@type":"Organization","name":null},"sourceOrganization":[{"@context":"https://schema.org","@type":"EducationalOrganization","name":null}],"thumbnailUrl":"https://attachments.academia-assets.com/67024372/thumbnails/1.jpg","url":"https://www.academia.edu/48382628/Models_of_experimental_evolution_the_role_of_genetic_chance_and_selective_necessity"}</script><link rel="stylesheet" media="all" 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"https://www.academia.edu/login?post_login_redirect_url=https%3A%2F%2Fwww.academia.edu%2F48382628%2FModels_of_experimental_evolution_the_role_of_genetic_chance_and_selective_necessity%3Fauto%3Ddownload"; window.loswp.translateUrl = "https://www.academia.edu/login?post_login_redirect_url=https%3A%2F%2Fwww.academia.edu%2F48382628%2FModels_of_experimental_evolution_the_role_of_genetic_chance_and_selective_necessity%3Fshow_translation%3Dtrue"; window.loswp.previewableAttachments = [{"id":67024372,"identifier":"Attachment_67024372","shouldShowBulkDownload":false}]; window.loswp.shouldDetectTimezone = true; window.loswp.shouldShowBulkDownload = true; window.loswp.showSignupCaptcha = false window.loswp.willEdgeCache = false; window.loswp.work = {"work":{"id":48382628,"created_at":"2021-05-04T16:03:57.303-07:00","from_world_paper_id":169632864,"updated_at":"2021-05-04T18:07:47.759-07:00","_data":{"abstract":"We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness inc...","publication_date":"2000,,","publication_name":"Genetics"},"document_type":"paper","pre_hit_view_count_baseline":null,"quality":"high","language":"en","title":"Models of experimental evolution: the role of genetic chance and selective necessity","broadcastable":false,"draft":null,"has_indexable_attachment":true,"indexable":true}}["work"]; window.loswp.workCoauthors = [41750952]; window.loswp.locale = "en"; window.loswp.countryCode = "SG"; window.loswp.cwvAbTestBucket = ""; window.loswp.designVariant = "ds_vanilla"; window.loswp.fullPageMobileSutdModalVariant = "full_page_mobile_sutd_modal"; window.loswp.useOptimizedScribd4genScript = false; window.loginModal = {}; window.loginModal.appleClientId = 'edu.academia.applesignon';</script><script defer="" src="https://accounts.google.com/gsi/client"></script><div class="ds-loswp-container"><div class="ds-work-card--grid-container"><div class="ds-work-card--container js-loswp-work-card"><div class="ds-work-card--cover"><div class="ds-work-cover--wrapper"><div class="ds-work-cover--container"><button class="ds-work-cover--clickable js-swp-download-button" data-signup-modal="{"location":"swp-splash-paper-cover","attachmentId":67024372,"attachmentType":"pdf"}"><img alt="First page of “Models of experimental evolution: the role of genetic chance and selective necessity”" class="ds-work-cover--cover-thumbnail" src="https://0.academia-photos.com/attachment_thumbnails/67024372/mini_magick20210504-26143-1kgnvg3.png?1620180774" /><img alt="PDF Icon" class="ds-work-cover--file-icon" src="//a.academia-assets.com/images/single_work_splash/adobe_icon.svg" /><div class="ds-work-cover--hover-container"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span><p>Download Free PDF</p></div><div class="ds-work-cover--ribbon-container">Download Free PDF</div><div class="ds-work-cover--ribbon-triangle"></div></button></div></div></div><div class="ds-work-card--work-information"><h1 class="ds-work-card--work-title">Models of experimental evolution: the role of genetic chance and selective necessity</h1><div class="ds-work-card--work-authors ds-work-card--detail"><a class="ds-work-card--author js-wsj-grid-card-author ds2-5-body-md ds2-5-body-link" data-author-id="41750952" href="https://independent.academia.edu/DavidKrakauer"><img alt="Profile image of David Krakauer" class="ds-work-card--author-avatar" src="https://0.academia-photos.com/41750952/29175492/27182084/s65_david.krakauer.jpg" />David Krakauer</a></div><div class="ds-work-card--detail"><p class="ds-work-card--detail ds2-5-body-sm">2000, Genetics</p><div class="ds-work-card--work-metadata"><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">visibility</span><p class="ds2-5-body-sm" id="work-metadata-view-count">…</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">description</span><p class="ds2-5-body-sm">12 pages</p></div><div class="ds-work-card--work-metadata__stat"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">link</span><p class="ds2-5-body-sm">1 file</p></div></div><script>(async () => { const workId = 48382628; 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if (!viewCountBody) { throw new Error('Failed to find work views element'); } viewCountBody.textContent = `${commaizedViewCount} views`; } catch (error) { // Remove the whole views element if there was some issue parsing. document.getElementById('work-metadata-view-count')?.parentNode?.remove(); throw new Error(`Failed to parse view count: ${viewCount}`, error); } }; // If the DOM is still loading, wait for it to be ready before updating the view count. if (document.readyState === "loading") { document.addEventListener('DOMContentLoaded', () => { updateViewCount(viewCount); }); // Otherwise, just update it immediately. } else { updateViewCount(viewCount); } })();</script></div><p class="ds-work-card--work-abstract ds-work-card--detail ds2-5-body-md">We present a theoretical framework within which to analyze the results of experimental evolution. Rapidly evolving organisms such as viruses, bacteria, and protozoa can be induced to adapt to laboratory conditions on very short human time scales. Artificial adaptive radiation is characterized by a list of common observations; we offer a framework in which many of these repeated questions and patterns can be characterized analytically. We allow for stochasticity by including rare mutations and bottleneck effects, demonstrating how these increase variability in the evolutionary trajectory. When the product Np, the population size times the per locus error rate, is small, the rate of evolution is limited by the chance occurrence of beneficial mutations; when Np is large and selective pressure is strong, the rate-limiting step is the waiting time while existing beneficial mutations sweep through the population. We derive the rate of divergence (substitution rate) and rate of fitness inc...</p><div class="ds-work-card--button-container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--work-card","attachmentId":67024372,"attachmentType":"pdf","workUrl":"https://www.academia.edu/48382628/Models_of_experimental_evolution_the_role_of_genetic_chance_and_selective_necessity"}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--work-card","attachmentId":67024372,"attachmentType":"pdf","workUrl":"https://www.academia.edu/48382628/Models_of_experimental_evolution_the_role_of_genetic_chance_and_selective_necessity"}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div></div><div data-auto_select="false" data-client_id="331998490334-rsn3chp12mbkiqhl6e7lu2q0mlbu0f1b" data-doc_id="67024372" data-landing_url="https://www.academia.edu/48382628/Models_of_experimental_evolution_the_role_of_genetic_chance_and_selective_necessity" data-login_uri="https://www.academia.edu/registrations/google_one_tap" data-moment_callback="onGoogleOneTapEvent" id="g_id_onload"></div><div class="ds-top-related-works--grid-container"><div class="ds-related-content--container ds-top-related-works--container"><h2 class="ds-related-content--heading">Related papers</h2><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="0" data-entity-id="11408096" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/11408096/Evaluating_the_impact_of_population_bottlenecks_in_experimental_evolution">Evaluating the impact of population bottlenecks in experimental evolution</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="27756131" href="https://mun.academia.edu/IvanSaikaVoivod">Ivan Saika-Voivod</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Genetics, 2002</p><p class="ds-related-work--abstract ds2-5-body-sm">Experimental evolution involves severe, periodic reductions in population size when fresh media are inoculated during serial transfer. These bottlenecks affect the dynamics of evolution, reducing the probability that a beneficial mutation will reach fixation. We quantify the impact of these bottlenecks on the evolutionary dynamics, for populations that grow exponentially between transfers and for populations in which growth is curbed by a resource-limited environment. We find that in both cases, mutations that survive bottlenecks are equally likely to occur, per unit time, at all times during the growth phase. We estimate the total fraction of beneficial mutations that are lost due to bottlenecks during experimental evolution protocols and derive the "optimal" dilution ratio, the ratio that maximizes the number of surviving beneficial mutations. Although more severe dilution ratios are often used in the literature, we find that a ratio of 0.1-0.2 minimizes the chances that rare beneficial mutations are lost. Finally, we provide a number of useful approximate results and illustrate our approach with applications to experimental evolution protocols in the literature.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Evaluating the impact of population bottlenecks in experimental evolution","attachmentId":46725431,"attachmentType":"pdf","work_url":"https://www.academia.edu/11408096/Evaluating_the_impact_of_population_bottlenecks_in_experimental_evolution","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/11408096/Evaluating_the_impact_of_population_bottlenecks_in_experimental_evolution"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="1" data-entity-id="94992790" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/94992790/Overabundant_mutations_help_potentiate_evolution_The_effect_of_biologically_realistic_mutation_rates_on_computer_models_of_evolution">Overabundant mutations help potentiate evolution: The effect of biologically realistic mutation rates on computer models of evolution</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="31139791" href="https://independent.academia.edu/WinstonEwert">Winston Ewert</a></div><p class="ds-related-work--metadata ds2-5-body-xs">BIO-Complexity, 2015</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Overabundant mutations help potentiate evolution: The effect of biologically realistic mutation rates on computer models of evolution","attachmentId":97298139,"attachmentType":"pdf","work_url":"https://www.academia.edu/94992790/Overabundant_mutations_help_potentiate_evolution_The_effect_of_biologically_realistic_mutation_rates_on_computer_models_of_evolution","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/94992790/Overabundant_mutations_help_potentiate_evolution_The_effect_of_biologically_realistic_mutation_rates_on_computer_models_of_evolution"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="2" data-entity-id="73111970" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/73111970/Evolution_of_evolvability_via_adaptation_of_mutation_rates">Evolution of evolvability via adaptation of mutation rates</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="48390059" href="https://unive.academia.edu/NormanPackard">Norman Packard</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Biosystems, 2003</p><p class="ds-related-work--abstract ds2-5-body-sm">We examine a simple form of the evolution of evolvability-the evolution of mutation rates-in a simple model system. The system is composed of many agents moving, reproducing, and dying in a two-dimensional resource-limited world. We first examine various macroscopic quantities (three types of genetic diversity, a measure of population fitness, and a measure of evolutionary activity) as a function of fixed mutation rates. The results suggest that (i) mutation rate is a control parameter that governs a transition between two qualitatively different phases of evolution, an ordered phase characterized by punctuated equilibria of diversity, and a disordered phase of characterized by noisy fluctuations around an equilibrium diversity, and (ii) the ability of evolution to create adaptive structure is maximized when the mutation rate is just below the transition between these two phases of evolution. We hypothesize that this transition occurs when the demands for evolutionary memory and evolutionary novelty are typically balanced. We next allow the mutation rate itself to evolve, and we observe that evolving mutation rates adapt to values at this transition. Furthermore, the mutation rates adapt up (or down) as the evolutionary demands for novelty (or memory) increase, thus supporting the balance hypothesis.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Evolution of evolvability via adaptation of mutation rates","attachmentId":81761579,"attachmentType":"pdf","work_url":"https://www.academia.edu/73111970/Evolution_of_evolvability_via_adaptation_of_mutation_rates","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/73111970/Evolution_of_evolvability_via_adaptation_of_mutation_rates"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="3" data-entity-id="14192866" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/14192866/Modeling_the_impact_of_periodic_bottlenecks_unidirectional_mutation_and_observational_error_in_experimental_evolution">Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="33208088" href="https://florida.academia.edu/Jos%C3%A9Ponciano">José Ponciano</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="33178215" href="https://independent.academia.edu/PaulJoyce2">Paul Joyce</a><span>, </span><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="33208391" href="https://uidaho.academia.edu/EvaTop">Eva Top</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Journal of Mathematical Biology, 2005</p><p class="ds-related-work--abstract ds2-5-body-sm">Antibiotic resistant bacteria are a constant threat in the battle against infectious diseases. One strategy for reducing their effect is to temporarily discontinue the use of certain antibiotics in the hope that in the absence of the antibiotic the resistant strains will be replaced by the sensitive strains. An experiment where this strategy is employed in vitro produces data which showed a slow accumulation of sensitive mutants. Here we propose a mathematical model and statistical analysis to explain this data.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution","attachmentId":44485094,"attachmentType":"pdf","work_url":"https://www.academia.edu/14192866/Modeling_the_impact_of_periodic_bottlenecks_unidirectional_mutation_and_observational_error_in_experimental_evolution","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/14192866/Modeling_the_impact_of_periodic_bottlenecks_unidirectional_mutation_and_observational_error_in_experimental_evolution"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="4" data-entity-id="12230503" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/12230503/A_Quantitative_Study_of_the_Dynamics_of_Adaptive_Mutation_Appearance">A Quantitative Study of the Dynamics of Adaptive Mutation Appearance</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="30730391" href="https://independent.academia.edu/EshelBenJacob">Eshel Ben-Jacob</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Physica A: Statistical …, 2001</p><p class="ds-related-work--abstract ds2-5-body-sm">We present two dynamical models for the appearance of adaptive mutations, which permit a quantitative comparison with experimental observations. The models quantify two alternative pictures: The hyper-mutating sub-population picture, and the population-wide mutation ...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"A Quantitative Study of the Dynamics of Adaptive Mutation Appearance","attachmentId":46292458,"attachmentType":"pdf","work_url":"https://www.academia.edu/12230503/A_Quantitative_Study_of_the_Dynamics_of_Adaptive_Mutation_Appearance","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/12230503/A_Quantitative_Study_of_the_Dynamics_of_Adaptive_Mutation_Appearance"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="5" data-entity-id="14938749" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/14938749/Dynamics_of_adaptation_and_diversification_a_10_000_generation_experiment_with_bacterial_populations">Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="33930957" href="https://michiganstate.academia.edu/RichardLenski">Richard Lenski</a></div><p class="ds-related-work--metadata ds2-5-body-xs">Proceedings of the National Academy of Sciences, 1994</p><p class="ds-related-work--abstract ds2-5-body-sm">We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences ofthe uniqueness ofevolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drit) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations","attachmentId":43729636,"attachmentType":"pdf","work_url":"https://www.academia.edu/14938749/Dynamics_of_adaptation_and_diversification_a_10_000_generation_experiment_with_bacterial_populations","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/14938749/Dynamics_of_adaptation_and_diversification_a_10_000_generation_experiment_with_bacterial_populations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="6" data-entity-id="35349331" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/35349331/The_repeatability_of_adaptive_radiation_during_long_term_experimental_evolution_of_Escherichia_coli_in_a_multiple_nutrient_environment">The repeatability of adaptive radiation during long-term experimental evolution of Escherichia coli in a multiple nutrient environment</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="20419182" href="https://spanalumni.academia.edu/MichaelTravisano">Michael Travisano</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PloS one, 2010</p><p class="ds-related-work--abstract ds2-5-body-sm">Adaptive radiations occur when a species diversifies into different ecological specialists due to competition for resources and trade-offs associated with the specialization. The evolutionary outcome of an instance of adaptive radiation cannot generally be predicted because chance (stochastic events) and necessity (deterministic events) contribute to the evolution of diversity. With increasing contributions of chance, the degree of parallelism among different instances of adaptive radiations and the predictability of an outcome will decrease. To assess the relative contributions of chance and necessity during adaptive radiation, we performed a selection experiment by evolving twelve independent microcosms of Escherichia coli for 1000 generations in an environment that contained two distinct resources. Specialization to either of these resources involves strong trade-offs in the ability to use the other resource. After selection, we measured three phenotypic traits: 1) fitness, 2) me...</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The repeatability of adaptive radiation during long-term experimental evolution of Escherichia coli in a multiple nutrient environment","attachmentId":55209878,"attachmentType":"pdf","work_url":"https://www.academia.edu/35349331/The_repeatability_of_adaptive_radiation_during_long_term_experimental_evolution_of_Escherichia_coli_in_a_multiple_nutrient_environment","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/35349331/The_repeatability_of_adaptive_radiation_during_long_term_experimental_evolution_of_Escherichia_coli_in_a_multiple_nutrient_environment"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="7" data-entity-id="124815174" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/124815174/The_evolutionary_origin_of_the_universal_distribution_of_mutation_fitness_effect">The evolutionary origin of the universal distribution of mutation fitness effect</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="194511207" href="https://independent.academia.edu/IgorRouzine">Igor Rouzine</a></div><p class="ds-related-work--metadata ds2-5-body-xs">PLOS Computational Biology, 2021</p><p class="ds-related-work--abstract ds2-5-body-sm">An intriguing fact long defying explanation is the observation of a universal exponential distribution of beneficial mutations in fitness effect for different microorganisms. To explain this effect, we use a population model including mutation, directional selection, linkage, and genetic drift. The multiple-mutation regime of adaptation at large population sizes (traveling wave regime) is considered. We demonstrate analytically and by simulation that, regardless of the inherent distribution of mutation fitness effect across genomic sites, an exponential distribution of fitness effects emerges in the long term. This result follows from the exponential statistics of the frequency of the less-fit alleles, f, that we predict to evolve, in the long term, for both polymorphic and monomorphic sites. We map the logarithmic slope of the distribution onto the previously derived fixation probability and demonstrate that it increases linearly in time. Our results demonstrate a striking difference between the distribution of fitness effects observed experimentally for naturally occurring mutations, and the "inherent" distribution obtained in a directed-mutagenesis experiment, which can have any shape depending on the organism. Based on these results, we develop a new method to measure the fitness effect of mutations for each variable residue using DNA sequences sampled from adapting populations. This new method is not sensitive to linkage effects and does not require the one-site model assumptions.</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"The evolutionary origin of the universal distribution of mutation fitness effect","attachmentId":118971052,"attachmentType":"pdf","work_url":"https://www.academia.edu/124815174/The_evolutionary_origin_of_the_universal_distribution_of_mutation_fitness_effect","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/124815174/The_evolutionary_origin_of_the_universal_distribution_of_mutation_fitness_effect"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="8" data-entity-id="1847068" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/1847068/Long_term_experimental_evolution_in_Escherichia_coli_I_Adaptation_and_divergence_during_2_000_generations">Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="480279" href="https://utah.academia.edu/ScottTadler">Scott C Tadler</a></div><p class="ds-related-work--metadata ds2-5-body-xs">American Naturalist, 1991</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations","attachmentId":25862835,"attachmentType":"pdf","work_url":"https://www.academia.edu/1847068/Long_term_experimental_evolution_in_Escherichia_coli_I_Adaptation_and_divergence_during_2_000_generations","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/1847068/Long_term_experimental_evolution_in_Escherichia_coli_I_Adaptation_and_divergence_during_2_000_generations"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div><div class="ds-related-work--container js-wsj-grid-card" data-collection-position="9" data-entity-id="79468986" data-sort-order="default"><a class="ds-related-work--title js-wsj-grid-card-title ds2-5-body-md ds2-5-body-link" href="https://www.academia.edu/79468986/Variation_in_fitness_in_molecular_evolution">Variation in fitness in molecular evolution</a><div class="ds-related-work--metadata"><a class="js-wsj-grid-card-author ds2-5-body-sm ds2-5-body-link" data-author-id="206002325" href="https://independent.academia.edu/sameerkujur3">sameer kujur</a></div><p class="ds-related-work--metadata ds2-5-body-xs">1972</p><div class="ds-related-work--ctas"><button class="ds2-5-text-link ds2-5-text-link--inline js-swp-download-button" data-signup-modal="{"location":"wsj-grid-card-download-pdf-modal","work_title":"Variation in fitness in molecular evolution","attachmentId":86173615,"attachmentType":"pdf","work_url":"https://www.academia.edu/79468986/Variation_in_fitness_in_molecular_evolution","alternativeTracking":true}"><span class="material-symbols-outlined" style="font-size: 18px" translate="no">download</span><span class="ds2-5-text-link__content">Download free PDF</span></button><a class="ds2-5-text-link ds2-5-text-link--inline js-wsj-grid-card-view-pdf" href="https://www.academia.edu/79468986/Variation_in_fitness_in_molecular_evolution"><span class="ds2-5-text-link__content">View PDF</span><span class="material-symbols-outlined" style="font-size: 18px" translate="no">chevron_right</span></a></div></div></div></div><div class="ds-sticky-ctas--wrapper js-loswp-sticky-ctas hidden"><div class="ds-sticky-ctas--grid-container"><div class="ds-sticky-ctas--container"><button class="ds2-5-button js-swp-download-button" data-signup-modal="{"location":"continue-reading-button--sticky-ctas","attachmentId":67024372,"attachmentType":"pdf","workUrl":null}">See full PDF</button><button class="ds2-5-button ds2-5-button--secondary js-swp-download-button" data-signup-modal="{"location":"download-pdf-button--sticky-ctas","attachmentId":67024372,"attachmentType":"pdf","workUrl":null}"><span class="material-symbols-outlined" style="font-size: 20px" translate="no">download</span>Download PDF</button></div></div></div><div class="ds-below-fold--grid-container"><div class="ds-work--container js-loswp-embedded-document"><div class="attachment_preview" data-attachment="Attachment_67024372" style="display: none"><div class="js-scribd-document-container"><div class="scribd--document-loading js-scribd-document-loader" style="display: block;"><img alt="Loading..." src="//a.academia-assets.com/images/loaders/paper-load.gif" /><p>Loading Preview</p></div></div><div style="text-align: center;"><div class="scribd--no-preview-alert js-preview-unavailable"><p>Sorry, preview is currently unavailable. 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