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Sequence — Evolution — Function

Author: Eugene V. Koonin

Publisher: Springer Science & Business Media

Published: 2013-06-29

Total Pages: 482

ISBN-13: 1475737831

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.

Models and Algorithms for Genome Evolution

Author: Cedric Chauve

Publisher: Springer Science & Business Media

Published: 2013-09-17

Total Pages: 329

ISBN-13: 1447152980

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This authoritative text/reference presents a review of the history, current status, and potential future directions of computational biology in molecular evolution. Gathering together the unique insights of an international selection of prestigious researchers, this must-read volume examines the latest developments in the field, the challenges that remain, and the new avenues emerging from the growing influx of sequence data. These viewpoints build upon the pioneering work of David Sankoff, one of the founding fathers of computational biology, and mark the 50th anniversary of his first scientific article. The broad spectrum of rich contributions in this essential collection will appeal to all computer scientists, mathematicians and biologists involved in comparative genomics, phylogenetics and related areas.

Introduction to Evolutionary Genomics

Author: Naruya Saitou

Publisher: Springer Science & Business Media

Published: 2014-01-22

Total Pages: 476

ISBN-13: 1447153049

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This book is the first of its kind to explain the fundamentals of evolutionary genomics. The comprehensive coverage includes concise descriptions of a variety of genome organizations, a thorough discussion of the methods used, and a detailed review of genome sequence processing procedures. The opening chapters also provide the necessary basics for readers unfamiliar with evolutionary studies. Features: introduces the basics of molecular biology, DNA replication, mutation, phylogeny, neutral evolution, and natural selection; presents a brief evolutionary history of life from the primordial seas to the emergence of humans; describes the genomes of prokaryotes, eukaryotes, vertebrates, and humans; reviews methods for genome sequencing, phenotype data collection, homology searches and analysis, and phylogenetic tree and network building; discusses databases of genome sequences and related information, evolutionary distances, and population genomics; provides supplementary material at an associated website.

The Origins of Genome Architecture

Author: Michael Lynch

Publisher: Sinauer

Published: 2007-06

Total Pages: 518

ISBN-13:

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The availability of genomic blueprints for hundreds of species has led to a transformation in biology, encouraging the proliferation of adaptive arguments for the evolution of genomic features. This text explains why the details matter and presents a framework for how the architectural diversity of eukaryotic genomes and genes came to arise.

Avian Genomics in Ecology and Evolution

Author: Robert H. S. Kraus

Publisher: Springer

Published: 2019-06-29

Total Pages: 348

ISBN-13: 3030164772

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Birds catch the public imagination like no other group of animals; in addition, birders are perhaps the largest non-professional naturalist community. Genomics and associated bioinformatics have revolutionised daily life in just a few decades. At the same time, this development has facilitated the application of genomics technology to ecological and evolutionary studies, including biodiversity and conservation at all levels. This book reveals how the exciting toolbox of genomics offers new opportunities in all areas of avian biology. It presents contributions from prominent experts at the intersection of avian biology and genomics, and offers an ideal introduction to the world of genomics for students, biologists and bird enthusiasts alike. The book begins with a historical perspective on how genomic technology was adopted by bird ecology and evolution research groups. This led, as the book explains, to a revised understanding of avian evolution, with exciting consequences for biodiversity research as a whole. Lastly, these impacts are illustrated using seminal examples and the latest discoveries from avian biology laboratories around the world.

Ecological Genomics

Author: Christian R. Landry

Publisher: Springer Science & Business Media

Published: 2013-11-25

Total Pages: 358

ISBN-13: 9400773471

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Researchers in the field of ecological genomics aim to determine how a genome or a population of genomes interacts with its environment across ecological and evolutionary timescales. Ecological genomics is trans-disciplinary by nature. Ecologists have turned to genomics to be able to elucidate the mechanistic bases of the biodiversity their research tries to understand. Genomicists have turned to ecology in order to better explain the functional cellular and molecular variation they observed in their model organisms. We provide an advanced-level book that covers this recent research and proposes future development for this field. A synthesis of the field of ecological genomics emerges from this volume. Ecological Genomics covers a wide array of organisms (microbes, plants and animals) in order to be able to identify central concepts that motivate and derive from recent investigations in different branches of the tree of life. Ecological Genomics covers 3 fields of research that have most benefited from the recent technological and conceptual developments in the field of ecological genomics: the study of life-history evolution and its impact of genome architectures; the study of the genomic bases of phenotypic plasticity and the study of the genomic bases of adaptation and speciation.

Polyploidy and Genome Evolution

Author: Pamela Soltis

Publisher: Springer Science & Business Media

Published: 2012-10-03

Total Pages: 416

ISBN-13: 3642314414

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Polyploidy – whole-genome duplication (WGD) – is a fundamental driver of biodiversity with significant consequences for genome structure, organization, and evolution. Once considered a speciation process common only in plants, polyploidy is now recognized to have played a major role in the structure, gene content, and evolution of most eukaryotic genomes. In fact, the diversity of eukaryotes seems closely tied to multiple WGDs. Polyploidy generates new genomic interactions – initially resulting in “genomic and transcriptomic shock” – that must be resolved in a new polyploid lineage. This process essentially acts as a “reset” button, resulting in genomic changes that may ultimately promote adaptive speciation. This book brings together for the first time the conceptual and theoretical underpinnings of polyploid genome evolution with syntheses of the patterns and processes of genome evolution in diverse polyploid groups. Because polyploidy is most common and best studied in plants, the book emphasizes plant models, but recent studies of vertebrates and fungi are providing fresh perspectives on factors that allow polyploid speciation and shape polyploid genomes. The emerging paradigm is that polyploidy – through alterations in genome structure and gene regulation – generates genetic and phenotypic novelty that manifests itself at the chromosomal, physiological, and organismal levels, with long-term ecological and evolutionary consequences.

Evolution of the Human Genome II

Author: Naruya Saitou

Publisher: Springer Nature

Published: 2021-05-27

Total Pages: 260

ISBN-13: 4431569049

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This two-volume set provides a general overview of the evolution of the human genome; The first volume overviews the human genome with descriptions of important gene groups. This second volume provides up-to-date, concise yet ample knowledge on the genome evolution of modern humans. It comprises twelve chapters divided into two parts discussing “Non-neutral Evolution on Human Genes” (Part I) and “Evolution of Modern Human Populations” (Part II.) The most significant feature of this book is the continent-wise discussion of modern human dispersal using human genomic data in Part II. Recent results such as introgression of paleogenomes to modern humans, new methods such as computer simulation of global human dispersals, and new information on genes for humanness will be of particular interest to the readers. Since the euchromatin regions of the human genome was sequenced in 2003, a huge number of research papers were published on modern human evolution for a variety of populations. It is now time to summarize these achievements. This book stands out as the most comprehensive book on the modern human evolution, focusing on genomic points of view with a broad scope. Primary target audiences are researchers and graduate students in evolutionary biology.

Genomic Control Process

Author: Isabelle S. Peter

Publisher: Academic Press

Published: 2015-01-21

Total Pages: 461

ISBN-13: 0124047467

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Genomic Control Process explores the biological phenomena around genomic regulatory systems that control and shape animal development processes, and which determine the nature of evolutionary processes that affect body plan. Unifying and simplifying the descriptions of development and evolution by focusing on the causality in these processes, it provides a comprehensive method of considering genomic control across diverse biological processes. This book is essential for graduate researchers in genomics, systems biology and molecular biology seeking to understand deep biological processes which regulate the structure of animals during development. Covers a vast area of current biological research to produce a genome oriented regulatory bioscience of animal life Places gene regulation, embryonic and postembryonic development, and evolution of the body plan in a unified conceptual framework Provides the conceptual keys to interpret a broad developmental and evolutionary landscape with precise experimental illustrations drawn from contemporary literature Includes a range of material, from developmental phenomenology to quantitative and logic models, from phylogenetics to the molecular biology of gene regulation, from animal models of all kinds to evidence of every relevant type Demonstrates the causal power of system-level understanding of genomic control process Conceptually organizes a constellation of complex and diverse biological phenomena Investigates fundamental developmental control system logic in diverse circumstances and expresses these in conceptual models Explores mechanistic evolutionary processes, illuminating the evolutionary consequences of developmental control systems as they are encoded in the genome

Ancestors in Our Genome

Author: Eugene E. Harris (Professor)

Publisher: Oxford University Press, USA

Published: 2015

Total Pages: 249

ISBN-13: 0199978034

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Geneticist Eugene Harris presents us with the complete and up-to-date account of the evolution of the human genome.