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The interdisciplinary field of Astrobiology constitutes a joint arena where provocative discoveries are coalescing concerning, e.g. the prevalence of exoplanets, the diversity and hardiness of life, and its increasingly likely chances for its emergence. Biologists, astrophysicists, biochemists, geoscientists and space scientists share this exciting mission of revealing the origin and commonality of life in the Universe. The members of the different disciplines are used to their own terminology and technical language. In the interdisciplinary environment many terms either have redundant meanings or are completely unfamiliar to members of other disciplines. The Encyclopedia of Astrobiology serves as the key to a common understanding. Each new or experienced researcher and graduate student in adjacent fields of astrobiology will appreciate this reference work in the quest to understand the big picture. The carefully selected group of active researchers contributing to this work and the expert field editors intend for their contributions, from an internationally comprehensive perspective, to accelerate the interdisciplinary advance of astrobiology.
In this New York Times bestseller and longlist nominee for the National Book Award, “our greatest living chronicler of the natural world” (The New York Times), David Quammen explains how recent discoveries in molecular biology affect our understanding of evolution and life’s history. In the mid-1970s, scientists began using DNA sequences to reexamine the history of all life. Perhaps the most startling discovery to come out of this new field—the study of life’s diversity and relatedness at the molecular level—is horizontal gene transfer (HGT), or the movement of genes across species lines. It turns out that HGT has been widespread and important; we now know that roughly eight percent of the human genome arrived sideways by viral infection—a type of HGT. In The Tangled Tree, “the grandest tale in biology….David Quammen presents the science—and the scientists involved—with patience, candor, and flair” (Nature). We learn about the major players, such as Carl Woese, the most important little-known biologist of the twentieth century; Lynn Margulis, the notorious maverick whose wild ideas about “mosaic” creatures proved to be true; and Tsutomu Wantanabe, who discovered that the scourge of antibiotic-resistant bacteria is a direct result of horizontal gene transfer, bringing the deep study of genome histories to bear on a global crisis in public health. “David Quammen proves to be an immensely well-informed guide to a complex story” (The Wall Street Journal). In The Tangled Tree, he explains how molecular studies of evolution have brought startling recognitions about the tangled tree of life—including where we humans fit upon it. Thanks to new technologies, we now have the ability to alter even our genetic composition—through sideways insertions, as nature has long been doing. “The Tangled Tree is a source of wonder….Quammen has written a deep and daring intellectual adventure” (The Boston Globe).
Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics. The book provides the reader with an understanding of the principles and approaches of functional genomics and of the potential and limitations of computational and experimental approaches to genome analysis. Sequence - Evolution - Function should help bridge the "digital divide" between biologists and computer scientists, allowing biologists to better grasp the peculiarities of the emerging field of Genome Biology and to learn how to benefit from the enormous amount of sequence data available in the public databases. The book is non-technical with respect to the computer methods for genome analysis and discusses these methods from the user's viewpoint, without addressing mathematical and algorithmic details. Prior practical familiarity with the basic methods for sequence analysis is a major advantage, but a reader without such experience will be able to use the book as an introduction to these methods. This book is perfect for introductory level courses in computational methods for comparative and functional genomics.
How small can a free-living organism be? On the surface, this question is straightforward-in principle, the smallest cells can be identified and measured. But understanding what factors determine this lower limit, and addressing the host of other questions that follow on from this knowledge, require a fundamental understanding of the chemistry and ecology of cellular life. The recent report of evidence for life in a martian meteorite and the prospect of searching for biological signatures in intelligently chosen samples from Mars and elsewhere bring a new immediacy to such questions. How do we recognize the morphological or chemical remnants of life in rocks deposited 4 billion years ago on another planet? Are the empirical limits on cell size identified by observation on Earth applicable to life wherever it may occur, or is minimum size a function of the particular chemistry of an individual planetary surface? These questions formed the focus of a workshop on the size limits of very small organisms, organized by the Steering .Group for the Workshop on Size Limits of Very Small Microorganisms and held on October 22 and 23, 1998. Eighteen invited panelists, representing fields ranging from cell biology and molecular genetics to paleontology and mineralogy, joined with an almost equal number of other participants in a wide-ranging exploration of minimum cell size and the challenge of interpreting micro- and nano-scale features of sedimentary rocks found on Earth or elsewhere in the solar system. This document contains the proceedings of that workshop. It includes position papers presented by the individual panelists, arranged by panel, along with a summary, for each of the four sessions, of extensive roundtable discussions that involved the panelists as well as other workshop participants.
Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.
Organic matter in aquatic environments consists mostly of large compounds which cannot be taken up and utilized directly by microbial cells. Prior to incorporation, polymeric materials undergo degradation by cell-bound and extracellular enzymes produced by these microbes; in fact, such enzymatic mobilization and transformation is the key process which regulates the turnover of organic as well as inorganic compounds in aquatic environments. This volume brings together studies on enzymatic degradation processes from disciplines as diverse as water and sediment research, bacterial and algal aquatic ecophysiology, eutrophication, and nutrient cycling and biogeochemistry, in both freshwater and marine ecosystems. Its scope extends from fundamental research exploring the contribution of microbial enzymatic processes to whole ecosystem functioning to practical applications in water biotechnology. The first comprehensive publication providing an overview of this emerging field of enzymology, Microbial Enzymes in Aquatic Environments will be of great interest to ecologists and microbiologists alike.
Written for non-experts, this volume introduces the mechanisms that underlie reticulate evolution. Chapters are either accompanied with glossaries that explain new terminology or timelines that position pioneering scholars and their major discoveries in their historical contexts. The contributing authors outline the history and original context of discovery of symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow and infectious heredity. By applying key insights from the areas of molecular (phylo)genetics, microbiology, virology, ecology, systematics, immunology, epidemiology and computational science, they demonstrate how reticulate evolution impacts successful survival, fitness and speciation. Reticulate evolution brings forth a challenge to the standard Neo-Darwinian framework, which defines life as the outcome of bifurcation and ramification patterns brought forth by the vertical mechanism of natural selection. Reticulate evolution puts forward a pattern in the tree of life that is characterized by horizontal mergings and lineage crossings induced by symbiosis, symbiogenesis, lateral gene transfer, hybridization or divergence with gene flow and infective heredity, making the “tree of life” look more like a “web of life.” On an epistemological level, the various means by which hereditary material can be transferred horizontally challenges our classic notions of units and levels of evolution, fitness, modes of transmission, linearity, communities and biological individuality. The case studies presented examine topics including the origin of the eukaryotic cell and its organelles through symbiogenesis; the origin of algae through primary and secondary symbiosis and dinoflagellates through tertiary symbiosis; the superorganism and holobiont as units of evolution; how endosymbiosis induces speciation in multicellular life forms; transferrable and non-transferrable plasmids and how they symbiotically interact with their host; the means by which pro- and eukaryotic organisms transfer genes laterally (bacterial transformation, transduction and conjugation as well as transposons and other mobile genetic elements); hybridization and divergence with gene flow in sexually-reproducing individuals; current (human) microbiome and viriome studies that impact our knowledge concerning the evolution of organismal health and acquired immunity; and how symbiosis and symbiogenesis can be modelled in computational evolution.
Nearly four decades ago Richard Dawkins published The Selfish Gene, famously reducing humans to “survival machines” whose sole purpose was to preserve “the selfish molecules known as genes.” How these selfish genes work together to construct the organism, however, remained a mystery. Standing atop a wealth of new research, The Society of Genes now provides a vision of how genes cooperate and compete in the struggle for life. Pioneers in the nascent field of systems biology, Itai Yanai and Martin Lercher present a compelling new framework to understand how the human genome evolved and why understanding the interactions among our genes shifts the basic paradigm of modern biology. Contrary to what Dawkins’s popular metaphor seems to imply, the genome is not made of individual genes that focus solely on their own survival. Instead, our genomes comprise a society of genes which, like human societies, is composed of members that form alliances and rivalries. In language accessible to lay readers, The Society of Genes uncovers genetic strategies of cooperation and competition at biological scales ranging from individual cells to entire species. It captures the way the genome works in cancer cells and Neanderthals, in sexual reproduction and the origin of life, always underscoring one critical point: that only by putting the interactions among genes at center stage can we appreciate the logic of life.
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.