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Population And Evolutionary Dynamics During Microbial Range Expansions
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Book Synopsis Population and Evolutionary Dynamics During Microbial Range Expansions by : Saurabh Rajendra Gandhi
Download or read book Population and Evolutionary Dynamics During Microbial Range Expansions written by Saurabh Rajendra Gandhi and published by . This book was released on 2019 with total page 98 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spatial expansions occur across multiple scales, from the expanding range of a species to the growth of tumors and microbial biofilms. In ecology, range expansions are becoming more frequent due to environmental changes and rare long distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Moreover, the evolution and potentially even the survival of an expanding population depends on its genetic diversity, which is also predicted to reduce drastically during range expansions. However, testing these quantitative predictions in natural populations is difficult because of large environmental variability and the inability of replicating historical processes. In this thesis, I describe the use of a microbial model system to gain a deeper understanding of spatial range expansions in a controlled and replicable setting. In particularly, I study the role of cooperative growth in spatial expansions. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution. For non-cooperative growth, the expansion dynamics are dominated by population growth at the low-density front, which pulls the expansion forward. I find these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher and Skellam, suitably adapted to my experimental system. However, as cooperativity increases, the expansions transition to being pushed, i.e. controlled by growth in the bulk as well as in the front. In addition to the population dynamics, cooperation within populations is also predicted to significantly alter the evolutionary fate of expanding populations. This difference in evolutionary dynamics within pulled and pushed waves is also studied experimentally.
Download or read book Eco-Evolutionary Dynamics written by and published by Academic Press. This book was released on 2014-08-12 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: The theme of this volume is to discuss Eco-evolutionary Dynamics. - Updates and informs the reader on the latest research findings - Written by leading experts in the field - Highlights areas for future investigation
Book Synopsis Evolutionary Dynamics in Microbial Colonies by : Matti Gralka
Download or read book Evolutionary Dynamics in Microbial Colonies written by Matti Gralka and published by . This book was released on 2018 with total page 268 pages. Available in PDF, EPUB and Kindle. Book excerpt: Traditionally, evolutionary biology has mostly taken a retrospective view, looking backwards in time to infer past evolutionary dynamics. Over the past 30 years, evolution experiments in the laboratory have become a valuable complementary technique to study evolution in real time. Microbial populations in shaken flasks are an ideal model system to do this, because their short generation times and easy reproducibility allow for the study of dozens to hundreds of replicates. Our understanding of microbial evolution in these simple laboratory environments has dramatically improved in recent years. Microbial populations in the wild face vastly more complex conditions: they grow as spatially structured communities called microbial biofilms, often consisting of interacting mixtures of different species fulfilling different purposes, subject to various, potentially self-generated, biophysicochemical gradients of, e.g., oxygen or nutrients, which are in turn altered by the physical structure of the community. In short, natural population are subject to a vast variety of ecological interactions, and it has remained unclear how much can be learned from well-mixed liquid culture experiments about how ecology affects evolution in more complex scenarios. In this dissertation, I approach this question using one of the simplest possible ecological aspects: the fact that most populations grow in spatially structured communities. Using microbial colonies as an experimental model system, I examine the effect of spatial structure on evolutionary dynamics in a variety of ways. First, Chapters 2-4 investigate the fates of neutral mutations and the dynamics of beneficial mutations in microbial colonies to find that both the neutral diversity resulting from spontaneous mutations and the strength of adaptation is increased in colonies compared to microbial populations grown in shaken flasks. The second half of the thesis is concerned with the effects of environmental heterogeneity on evolutionary dynamics. In Chapter 5, randomly disordered environments are used to examine the competition of selection and extrinsic noise in a model system for spontaneous beneficial and deleterious mutations. In these experiments, extrinsic noise can almost entirely overpower selection such that beneficial variants cannot leverage their advantage to further their evolutionary success. Chapter 6 discusses the effects of gradients on the emergence of antibiotic resistance and how convective flow can shape the trade-off between selection for resistance and the efficacy of treatment. Overall, the results presented in this thesis suggest that spatial structure can have a momentous influence on the evolutionary dynamics of many dense cellular populations like biofilms and tumors: not only do the dynamics of adaptation change quantitatively in spatially structured populations, but qualitatively different patterns of evolutionary dynamics emerge that cannot arise in well-mixed population. Environmental heterogeneity can also have a strong influence on the speed and the direction of adaptation: whereas random heterogeneity in the environment prevents the spread of beneficial variants, the presence of antibiotic gradients can facilitate the rapid emergence of resistance. This work thus offers a glimpse into the profound and complex ways in which ecology can impact evolution even in simple model systems.
Book Synopsis Dispersal Ecology and Evolution by : Jean Clobert
Download or read book Dispersal Ecology and Evolution written by Jean Clobert and published by OUP Oxford. This book was released on 2012-09-27 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: Now that so many ecosystems face rapid and major environmental change, the ability of species to respond to these changes by dispersing or moving between different patches of habitat can be crucial to ensuring their survival. Understanding dispersal has become key to understanding how populations may persist. Dispersal Ecology and Evolution provides a timely and wide-ranging overview of the fast expanding field of dispersal ecology, incorporating the very latest research. The causes, mechanisms, and consequences of dispersal at the individual, population, species, and community levels are considered. Perspectives and insights are offered from the fields of evolution, behavioural ecology, conservation biology, and genetics. Throughout the book theoretical approaches are combined with empirical data, and care has been taken to include examples from as wide a range of species as possible - both plant and animal.
Book Synopsis Eco-evolutionary Dynamics by : Andrew P. Hendry
Download or read book Eco-evolutionary Dynamics written by Andrew P. Hendry and published by Princeton University Press. This book was released on 2020-06-09 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, scientists have realized that evolution can occur on timescales much shorter than the 'long lapse of ages' emphasized by Darwin - in fact, evolutionary change is occurring all around us all the time. This work provides an authoritative and accessible introduction to eco-evolutionary dynamics, a cutting-edge new field that seeks to unify evolution and ecology into a common conceptual framework focusing on rapid and dynamic environmental and evolutionary change.
Book Synopsis On the Dynamics of Exploited Fish Populations by : Raymond J.H. Beverton
Download or read book On the Dynamics of Exploited Fish Populations written by Raymond J.H. Beverton and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 541 pages. Available in PDF, EPUB and Kindle. Book excerpt: Among the fishes, a remarkably wide range of biological adaptations to diverse habitats has evolved. As well as living in the conventional habitats of lakes, ponds, rivers, rock pools and the open sea, fish have solved the problems of life in deserts, in the deep sea, in the cold antarctic, and in warm waters of high alkalinity or of low oxygen. Along with these adaptations, we find the most impressive specializations of morphology, physiology and behaviour. For example we can marvel at the high-speed swimming of the marlins, sailfish and warm-blooded tunas, air-breathing in catfish and lungfish, parental care in the mouth-brooding cichlids, and viviparity in many sharks and toothcarps. Moreover, fish are of considerable importance to the survival of the human species in the form of nutritious, delicious and diverse food. Rational exploitation and management of our global stocks of fishes must rely upon a detailed and precise insight of their biology. The Chapman & Hall Fish and Fisheries Series aims to present timely volumes reviewing important aspects of fish biology. Most volumes will be of interest to research workers in biology, zoology, ecology and physiology but an additional aim is for the books to be accessible to a wide spectrum of non-specialist readers ranging from undergraduates and postgraduates to those with an interest in industrial and commercial aspects of fish and fisheries.
Book Synopsis Microbial Evolution by : Howard Ochman
Download or read book Microbial Evolution written by Howard Ochman and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria have been the dominant forms of life on Earth for the past 3.5 billion years. They rapidly evolve, constantly changing their genetic architecture through horizontal DNA transfer and other mechanisms. Consequently, it can be difficult to define individual species and determine how they are related. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines how bacteria and other microbes evolve, focusing on insights from genomics-based studies. Contributors discuss the origins of new microbial populations, the evolutionary and ecological mechanisms that keep species separate once they have diverged, and the challenges of constructing phylogenetic trees that accurately reflect their relationships. They describe the organization of microbial genomes, the various mutations that occur, including the birth of new genes de novo and by duplication, and how natural selection acts on those changes. The role of horizontal gene transfer as a strong driver of microbial evolution is emphasized throughout. The authors also explore the geologic evidence for early microbial evolution and describe the use of microbial evolution experiments to examine phenomena like natural selection. This volume will thus be essential reading for all microbial ecologists, population geneticists, and evolutionary biologists.
Download or read book The Pangenome written by Hervé Tettelin and published by Springer Nature. This book was released on 2020-04-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
Book Synopsis Adaptive Diversification by : Michael Doebeli
Download or read book Adaptive Diversification written by Michael Doebeli and published by Princeton University Press. This book was released on 2011-08-01 with total page 346 pages. Available in PDF, EPUB and Kindle. Book excerpt: Understanding the mechanisms driving biological diversity remains a central problem in ecology and evolutionary biology. Traditional explanations assume that differences in selection pressures lead to different adaptations in geographically separated locations. This book takes a different approach and explores adaptive diversification--diversification rooted in ecological interactions and frequency-dependent selection. In any ecosystem, birth and death rates of individuals are affected by interactions with other individuals. What is an advantageous phenotype therefore depends on the phenotype of other individuals, and it may often be best to be ecologically different from the majority phenotype. Such rare-type advantage is a hallmark of frequency-dependent selection and opens the scope for processes of diversification that require ecological contact rather than geographical isolation. Michael Doebeli investigates adaptive diversification using the mathematical framework of adaptive dynamics. Evolutionary branching is a paradigmatic feature of adaptive dynamics that serves as a basic metaphor for adaptive diversification, and Doebeli explores the scope of evolutionary branching in many different ecological scenarios, including models of coevolution, cooperation, and cultural evolution. He also uses alternative modeling approaches. Stochastic, individual-based models are particularly useful for studying adaptive speciation in sexual populations, and partial differential equation models confirm the pervasiveness of adaptive diversification. Showing that frequency-dependent interactions are an important driver of biological diversity, Adaptive Diversification provides a comprehensive theoretical treatment of adaptive diversification.
Book Synopsis Exploring Multispecies Evolutionary Dynamics Using Model Microbial Ecosystems by : Hasan Celiker
Download or read book Exploring Multispecies Evolutionary Dynamics Using Model Microbial Ecosystems written by Hasan Celiker and published by . This book was released on 2014 with total page 85 pages. Available in PDF, EPUB and Kindle. Book excerpt: Experiments to date probing adaptive evolution have predominantly focused on studying a single species or a pair of species in isolation. In nature, on the other hand, species evolve within complex communities, interacting and competing with many other species. We developed experimental microbial ecosystems with which we can start to answer some of the fundamental questions regarding evolution in complex ecosystems. We first tested how the evolution of cooperation within a species can be affected by the presence of competitor species in an ecosystem. To achieve this, we used sucrose metabolism of budding yeast, Saccharomyces cerevisiae, as a model cooperative system that is subject to social parasitism by cheater strategies. We found that when co-cultured with a bacterial competitor, Escherichia coli, the frequency of cooperator phenotypes in yeast populations increases dramatically as compared to isolated yeast populations. These results indicate that a thorough understanding of species interactions is crucial for explaining the maintenance and evolution of cooperation in nature. Next, we wanted to explore the question of whether evolution in a multispecies community is deterministic or random. We let many replicates of a multispecies laboratory bacterial ecosystem evolve in parallel for hundreds of generations. We found that after evolution, relative abundances of individual species varied greatly across the evolved ecosystems and that the final profile of species frequencies within replicates clustered into several distinct types, as opposed to being randomly dispersed across the frequency space or converging fully. These results suggest that community structure evolution has a tendency to follow one of only a few distinct paths.
Book Synopsis Population Genetics by : John H. Gillespie
Download or read book Population Genetics written by John H. Gillespie and published by JHU Press. This book was released on 2004-08-06 with total page 263 pages. Available in PDF, EPUB and Kindle. Book excerpt: Publisher Description
Book Synopsis Bacteriophages in Health and Disease by : Paul Hyman
Download or read book Bacteriophages in Health and Disease written by Paul Hyman and published by CABI. This book was released on 2012 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteriophages are viruses that infect bacteria; as such, they have many potential uses for promoting health and combating disease. This book covers the many facets of phage-bacterial-human interaction in three sections: the role and impact of phages on natural bacterial communities, the potential to develop phage-based therapeutics and other aspects in which phages can be used to combat disease, including bacterial detection, bacterial epidemiology, the tracing of fecal contamination of water and decontamination of foods.
Book Synopsis Dynamics of Fractal Surfaces by : Fereydoon Family
Download or read book Dynamics of Fractal Surfaces written by Fereydoon Family and published by World Scientific. This book was released on 1991 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last few years there has been an explosion of activity in the field of the dynamics of fractal surfaces, which, through the convergence of important new results from computer simulations, analytical theories and experiments, has led to significant advances in our understanding of nonequilibrium surface growth phenomena. This interest in surface growth phenomena has been motivated largely by the fact that a wide variety of natural and industrial processes lead to the formation of rough surfaces and interfaces. This book presents these developments in a single volume by bringing together the works containing the most important results in the field.The material is divided into chapters consisting of reprints related to a single major topic. Each chapter has a general introduction to a particular aspect of growing fractal surfaces. These introductory parts are included in order to provide a scientific background to the papers reproduced in the main part of the chapters. They are written in a pedagogical style and contain only the most essential information. The contents of the reprints are made more accessible to the reader as they are preceded by a short description of what the editors find to be the most significant results in the paper.
Book Synopsis Quantifying Evolutionary Dynamics by : Lukas Geyrhofer
Download or read book Quantifying Evolutionary Dynamics written by Lukas Geyrhofer and published by . This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Adaptation is a central process in evolution: populations adapt to their environment by accumulating beneficial mutations over the course of generations. Microbial populations present an excellent experimental system that allows to observe the adaptation process on reasonable timescales. Recent results of evolutionary experiments with microbes expose an intricate dynamics: beneficial mutations appear continuously and often many of them are present simultaneously. These different clones interfere on their way to fixation or extinction in the mostly asexually reproducing populations. This dyn ...
Download or read book Spatial Ecology written by David Tilman and published by Princeton University Press. This book was released on 2018-06-05 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spatial Ecology addresses the fundamental effects of space on the dynamics of individual species and on the structure, dynamics, diversity, and stability of multispecies communities. Although the ecological world is unavoidably spatial, there have been few attempts to determine how explicit considerations of space may alter the predictions of ecological models, or what insights it may give into the causes of broad-scale ecological patterns. As this book demonstrates, the spatial structure of a habitat can fundamentally alter both the qualitative and quantitative dynamics and outcomes of ecological processes. Spatial Ecology highlights the importance of space to five topical areas: stability, patterns of diversity, invasions, coexistence, and pattern generation. It illustrates both the diversity of approaches used to study spatial ecology and the underlying similarities of these approaches. Over twenty contributors address issues ranging from the persistence of endangered species, to the maintenance of biodiversity, to the dynamics of hosts and their parasitoids, to disease dynamics, multispecies competition, population genetics, and fundamental processes relevant to all these cases. There have been many recent advances in our understanding of the influence of spatially explicit processes on individual species and on multispecies communities. This book synthesizes these advances, shows the limitations of traditional, non-spatial approaches, and offers a variety of new approaches to spatial ecology that should stimulate ecological research.
Book Synopsis Stochastic Population Dynamics in Ecology and Conservation by : Russell Lande
Download or read book Stochastic Population Dynamics in Ecology and Conservation written by Russell Lande and published by OUP Oxford. This book was released on 2003 with total page 698 pages. Available in PDF, EPUB and Kindle. Book excerpt: 1. Demographic and environmental stochasticity -- 2. Extinction dynamics -- 3. Age structure -- 4. Spatial structure -- 5. Population viability analysis -- 6. Sustainable harvesting -- 7. Species diversity -- 8. Community dynamics.
Book Synopsis Quantifying Dynamics of Microbial Evolution for Nascent Beneficial Mutations in Barcode Lineage Tracking Experiment by : Huan-Yu Kuo
Download or read book Quantifying Dynamics of Microbial Evolution for Nascent Beneficial Mutations in Barcode Lineage Tracking Experiment written by Huan-Yu Kuo and published by . This book was released on 2023 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantifying the evolutionary dynamics of beneficial mutations in microbial populations relies on a massive sampling of nascent mutations, which has recently become possible by innovative barcode techniques. Despite barcode lineage tracking (BLT) experiments offer a straightforward means of capturing mutation frequency trajectories, accurately quantifying their dynamics remains a challenge. This dissertation addresses the critical issue of precisely and accurately estimating the fitness effects, mutation rates, and the distribution of fitness effects (DFE) associated with beneficial mutations identified in BLT experiments. First, I investigate the limitations of existing methods used to infer fitness effects and identify potential reasons for failure. To address this issue, I develop a novel Bayesian filtering method for fitness inference, which significantly enhances the accuracy of estimation compared to current approaches. Secondly, to estimate the rate of beneficial mutations within specific classes, I develop a stochastic model of mutant population dynamics. By applying this model, I infer the rate of beneficial mutations in the BLT experiment, providing valuable insights into mutation dynamics. Lastly, I highlight an inherent bias in our observations of beneficial mutations through adaptive evolution relative to the true underlying DFE. To address this disparity, I propose a method for inferring the mutation rate spectrum by back-calculating the observed DFE. The work presented in this dissertation establishes a statistically solid foundation for the analysis of the BLT experiment.
