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Author: Benjamin Jesse Shapiro
Publisher:
ISBN:
Category :
Languages : en
Pages : 228
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Book Description
Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared using the tools of population genetics to infer important genetic changes allowing them to diversify ecologically and adapt to distinct ecological niches. Yet the toolkit of population genetics was developed largely with sexual eukaryotes in mind. In this work, I assess and develop tools for inferring natural selection in microbial genomes. Many tools rely on population genetics theory, and thus require defining distinct populations, or species, of bacteria. Because sex (recombination) is not required for reproduction, some bacteria recombine only rarely, while others are extremely promiscuous, exchanging genes across great genetic distances. This behavior poses a challenge for defining microbial population boundaries. This thesis begins with a discussion of how recombination and positive selection interact to promote ecological adaptation. I then describe a general pipeline for quantifying the impacts of mutation, recombination and selection on microbial genomes, and apply it to two closely related, yet ecologically distinct populations of Vibrio splendidus, each with its own microhabitat preference. I introduce a new tool, STARRInIGHTS, for inferring homologous recombination events. By assessing rates of recombination within and between ecological populations, I conclude that ecological differentiation is driven by small number of habitat-specific alleles, while most loci are shared freely across habitats. The remainder of the thesis focuses on lineage-specific changes in natural selection among anciently diverged species of gamma proteobacteria. I develop two new metrics, selective signatures and slow:fast, for detecting deviations from the expected rate of evolution in 'core' proteins (present in single copy in most species). Because they rely on empirical distributions of evolutionary rates across species, these methods should become increasingly powerful as more and more microbial genomes are sampled. Overall, the methods described here significantly expand the repertoire of tools available for microbial population genomics, both for investigating the process of ecological differentiation at the finest of time scales, and over billions of years of microbial evolution.
Author: Benjamin Jesse Shapiro
Publisher:
ISBN:
Category :
Languages : en
Pages : 228
Get Book Here
Book Description
Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared using the tools of population genetics to infer important genetic changes allowing them to diversify ecologically and adapt to distinct ecological niches. Yet the toolkit of population genetics was developed largely with sexual eukaryotes in mind. In this work, I assess and develop tools for inferring natural selection in microbial genomes. Many tools rely on population genetics theory, and thus require defining distinct populations, or species, of bacteria. Because sex (recombination) is not required for reproduction, some bacteria recombine only rarely, while others are extremely promiscuous, exchanging genes across great genetic distances. This behavior poses a challenge for defining microbial population boundaries. This thesis begins with a discussion of how recombination and positive selection interact to promote ecological adaptation. I then describe a general pipeline for quantifying the impacts of mutation, recombination and selection on microbial genomes, and apply it to two closely related, yet ecologically distinct populations of Vibrio splendidus, each with its own microhabitat preference. I introduce a new tool, STARRInIGHTS, for inferring homologous recombination events. By assessing rates of recombination within and between ecological populations, I conclude that ecological differentiation is driven by small number of habitat-specific alleles, while most loci are shared freely across habitats. The remainder of the thesis focuses on lineage-specific changes in natural selection among anciently diverged species of gamma proteobacteria. I develop two new metrics, selective signatures and slow:fast, for detecting deviations from the expected rate of evolution in 'core' proteins (present in single copy in most species). Because they rely on empirical distributions of evolutionary rates across species, these methods should become increasingly powerful as more and more microbial genomes are sampled. Overall, the methods described here significantly expand the repertoire of tools available for microbial population genomics, both for investigating the process of ecological differentiation at the finest of time scales, and over billions of years of microbial evolution.
Author: Hervé Tettelin
Publisher: Springer Nature
ISBN: 3030382818
Category : Science
Languages : en
Pages : 311
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Book Description
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.
Author: David L. Jameson
Publisher:
ISBN:
Category : Evolution
Languages : en
Pages : 360
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Book Description
The nature of populations, races, subspecies, and species. Genetic basis of isolation. Origin of isolation - theoretical. Origin of isolation - experimental. The nature of the speciation process.
Author: David A. Baum
Publisher: Princeton University Press
ISBN: 1400848067
Category : Science
Languages : en
Pages : 888
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Book Description
The Princeton Guide to Evolution is a comprehensive, concise, and authoritative reference to the major subjects and key concepts in evolutionary biology, from genes to mass extinctions. Edited by a distinguished team of evolutionary biologists, with contributions from leading researchers, the guide contains some 100 clear, accurate, and up-to-date articles on the most important topics in seven major areas: phylogenetics and the history of life; selection and adaptation; evolutionary processes; genes, genomes, and phenotypes; speciation and macroevolution; evolution of behavior, society, and humans; and evolution and modern society. Complete with more than 100 illustrations (including eight pages in color), glossaries of key terms, suggestions for further reading on each topic, and an index, this is an essential volume for undergraduate and graduate students, scientists in related fields, and anyone else with a serious interest in evolution. Explains key topics in some 100 concise and authoritative articles written by a team of leading evolutionary biologists Contains more than 100 illustrations, including eight pages in color Each article includes an outline, glossary, bibliography, and cross-references Covers phylogenetics and the history of life; selection and adaptation; evolutionary processes; genes, genomes, and phenotypes; speciation and macroevolution; evolution of behavior, society, and humans; and evolution and modern society
Author: Roger Butlin
Publisher: Cambridge University Press
ISBN: 9780521709637
Category : Science
Languages : en
Pages : 346
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Book Description
The diversity of species of plants and animals is the net result of the origin of new species by the splitting of existing lineages (speciation) and the loss of species through extinction. Why there are more species in some groups of organisms, in some places or at some times depends on the balance of these processes. This book explores the interaction between mechanisms and rates of speciation and these patterns of biological diversity, and is unusual in that it brings together the viewpoints of ecologists interested in the processes that generate patterns of diversity and evolutionary biologists who focus on mechanisms of speciation. It is intended to stimulate dialogue between these groups and so promote a more complete understanding of biological diversity.
Author: Institute of Medicine
Publisher: National Academies Press
ISBN: 0309264324
Category : Medical
Languages : en
Pages : 633
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Book Description
Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.
Author: John Tyler Bonner
Publisher: Princeton University Press
ISBN: 9780691139395
Category : Science
Languages : en
Pages : 164
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Book Description
Noted biologist and author John Tyler Bonner has experimented with cellular slime molds for more than sixty years, and he has done more than anyone else to raise these peculiar collections of amoebae from a minor biological curiosity to a major model organism--one that is widely studied for clues to the development and evolution of all living things. Now, five decades after he published his first pioneering book on cellular slime molds, Bonner steps back from the proliferating and increasingly specialized knowledge about the organism to provide a broad, nontechnical picture of its whole biology, including its evolution, sociobiology, ecology, behavior, and development. The Social Amoebae draws the big lessons from decades of research, and shows how slime molds fit into and illuminate biology as a whole. Slime molds are very different from other organisms; they feed as individual amoebae before coming together to form a multicellular organism that has a remarkable ability to move and orient itself in its environment. Furthermore, these social amoebae display a sophisticated division of labor; within each organism, some cells form the stalk and others become the spores that will seed the next generation. In The Social Amoebae, Bonner examines all these parts together, giving a balanced, concise, and clear overview of slime mold biology, from molecules to cells to multicells, as he advances some unconventional and unexpected insights.
Author: Andrew Austin
Publisher: CSIRO PUBLISHING
ISBN: 9780643066106
Category : Science
Languages : en
Pages : 488
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Book Description
The Hymenoptera is one of the largest orders of terrestrial anthropods and compromises the sawflies, wasps, ants, bees and parasitic wasps. This book examines the current state of all major areas of research for this important group of insects, including systematics, biological control, behaviour and use in education.
Author: Therese A. Markow
Publisher: Elsevier
ISBN: 0080454097
Category : Science
Languages : en
Pages : 268
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Book Description
Anyone wishing to tap the research potential of the hundreds of Drosophila species in addition to D.melanogaster will finally have a single comprehensive resource for identifying, rearing and using this diverse group of insects. This is the only group of higher eukaryotes for which the genomes of 12 species have been sequenced.The fruitfly Drosophila melanogaster continues to be one of the greatest sources of information regarding the principles of heredity that apply to all animals, including humans. In reality, however, over a thousand different species of Drosophila exist, each with the potential to make their own unique contributions to the rapidly changing fields of genetics and evolution. This book, by providing basic information on how to identify and breed these other fruitflies, will allow investigators to take advantage, on a large scale, of the valuable qualities of these other Drosophila species and their newly developed genomic resources to address critical scientific questions.* Provides easy to use keys and illustrations to identify different Drosophila species* A guide to the life history differences of hundreds of species* Worldwide distribution maps of hundreds of species* Complete recipes for different Drosophila diets* Offers an analysis on how to account for species differences in designing and conducting experiments* Presents useful ideas of how to collect the many different Drosophila species in the wild
Author:
Publisher:
ISBN: 9780195122008
Category : Evolution (Biology)
Languages : en
Pages : 1205
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Book Description
Review: "All aspects of evolution, including theories, researchers, history, philosophy, processes, plants, and animals, are covered in this reference work. Other science reference publications include information about evolution, but this source is unique because of its comprehensive and thorough examination of the subject. It includes thought-provoking essays on such topics as culture in chimpanzees, motherhood, and Darwinian medicine, all written by recognized scholars in the fields. Extensive indexing makes any topic easy to locate. This is a crucial research tool for anyone in search of information on any aspect of evolution."--"The Best of the Best Reference Sources," American Libraries, May 2003
