Population Genomics

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Population Genomics

Om P. Rajora
Population Genomics Book PDF

Author : Om P. Rajora
Publisher : Springer
Page : 822 pages
File Size : 41,9 Mb
Release : 2019-01-07
Category : Science
ISBN : 9783030045890

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Population Genomics by Om P. Rajora Pdf

Population genomics has revolutionized various disciplines of biology including population, evolutionary, ecological and conservation genetics, plant and animal breeding, human health, medicine and pharmacology by allowing to address novel and long-standing questions with unprecedented power and accuracy. It employs large-scale or genome-wide genetic information and bioinformatics to address various fundamental and applied aspects in biology and related disciplines, and provides a comprehensive genome-wide perspective and new insights that were not possible before. These advances have become possible due to the development of new and low-cost sequencing and genotyping technologies and novel statistical approaches and software, bioinformatics tools, and models. Population genomics is tremendously advancing our understanding the roles of evolutionary processes, such as mutation, genetic drift, gene flow, and natural selection, in shaping up genetic variation at individual loci and across the genome and populations; improving the assessment of population genetic parameters or processes such as adaptive evolution, effective population size, gene flow, admixture, inbreeding and outbreeding depression, demography, and biogeography; resolving evolutionary histories and phylogenetic relationships of extant, ancient and extinct species; understanding the genomic basis of fitness, adaptation, speciation, complex ecological and economically important traits, and disease and insect resistance; facilitating forensics, genetic medicine and pharmacology; delineating conservation genetic units; and understanding the genetic effects of resource management practices, and assisting conservation and sustainable management of genetic resources. This Population Genomics book discusses the concepts, approaches, applications and promises of population genomics in addressing most of the above fundamental and applied crucial aspects in a variety of organisms from microorganisms to humans. The book provides insights into a range of emerging population genomics topics including population epigenomics, landscape genomics, seascape genomics, paleogenomics, ecological and evolutionary genomics, biogeography, demography, speciation, admixture, colonization and invasion, genomic selection, and plant and animal domestication. This book fills a vacuum in the field and is expected to become a primary reference in Population Genomics world-wide.

Statistical Population Genomics

Julien Y Dutheil
Statistical Population Genomics Book PDF

Author : Julien Y Dutheil
Publisher : Unknown
Page : 464 pages
File Size : 52,9 Mb
Release : 2020-10-08
Category : Science
ISBN : 1013271408

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Statistical Population Genomics by Julien Y Dutheil Pdf

This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.

Population Genomics: Marine Organisms

Marjorie F. Oleksiak,Om P. Rajora
Population Genomics Marine Organisms Book PDF

Author : Marjorie F. Oleksiak,Om P. Rajora
Publisher : Springer Nature
Page : 458 pages
File Size : 54,8 Mb
Release : 2019-12-31
Category : Science
ISBN : 9783030379360

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Population Genomics: Marine Organisms by Marjorie F. Oleksiak,Om P. Rajora Pdf

Population genomics has provided unprecedented opportunities to unravel the mysteries of marine organisms in the oceans' depths. The world's oceans, which make up 70% of our planet, encompass diverse habitats and host numerous unexplored populations and species. Population genomics studies of marine organisms are rapidly emerging and have the potential to transform our understanding of marine populations, species, and ecosystems, providing insights into how these organisms are evolving and how they respond to different stimuli and environments. This knowledge is critical for understanding the fundamental aspects of marine life, how marine organisms will respond to environmental changes, and how we can better protect and preserve marine biodiversity and resources. This book brings together leading experts in the field to address critical aspects of fundamental and applied research in marine species and share their research and insights crucial for understanding marine ecosystem diversity and function. It also discusses the challenges, opportunities and future perspectives of marine population genomics.

Population Genomics: Wildlife

Paul A. Hohenlohe,Om P. Rajora
Population Genomics Wildlife Book PDF

Author : Paul A. Hohenlohe,Om P. Rajora
Publisher : Springer Nature
Page : 559 pages
File Size : 46,8 Mb
Release : 2020-12-09
Category : Science
ISBN : 9783030634896

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Population Genomics: Wildlife by Paul A. Hohenlohe,Om P. Rajora Pdf

Population genomics is revolutionizing wildlife biology, conservation, and management by providing key and novel insights into genetic, population and landscape-level processes in wildlife, with unprecedented power and accuracy. This pioneering book presents the advances and potential of population genomics in wildlife, outlining key population genomics concepts and questions in wildlife biology, population genomics approaches that are specifically applicable to wildlife, and application of population genomics in wildlife population and evolutionary biology, ecology, adaptation and conservation and management. It is important for students, researchers, and wildlife professionals to understand the growing set of population genomics tools that can address issues from delineation of wildlife populations to assessing their capacity to adapt to environmental change. This book brings together leading experts in wildlife population genomics to discuss the key areas of the field, as well as challenges, opportunities and future prospects of wildlife population genomics.

Population Genomics with R

Emmanuel Paradis
Population Genomics with R Book PDF

Author : Emmanuel Paradis
Publisher : CRC Press
Page : 395 pages
File Size : 50,7 Mb
Release : 2020-05-05
Category : Mathematics
ISBN : 9780429882432

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Population Genomics with R by Emmanuel Paradis Pdf

Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).

Human Population Genomics

Kirk E. Lohmueller,Rasmus Nielsen
Human Population Genomics Book PDF

Author : Kirk E. Lohmueller,Rasmus Nielsen
Publisher : Springer Nature
Page : 236 pages
File Size : 47,5 Mb
Release : 2021-03-13
Category : Science
ISBN : 9783030616465

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Human Population Genomics by Kirk E. Lohmueller,Rasmus Nielsen Pdf

This textbook provides a concise introduction and useful overview of the field of human population genomics, making the highly technical and contemporary aspects more accessible to students and researchers from various fields. Over the past decade, there has been a deluge of genetic variation data from the entire genome of individuals from many populations. These data have allowed an unprecedented look at human history and how natural selection has impacted humans during this journey. Simultaneously, there have been increased efforts to determine how genetic variation affects complex traits in humans. Due to technological and methodological advances, progress has been made at determining the architecture of complex traits. Split in three parts, the book starts with the basics, followed by more advanced and current research. The first part provides an introduction to essential concepts in population genetics, which are relevant for any organism. The second part covers the genetics of complex traits in humans. The third part focuses on applying these techniques and concepts to genetic variation data to learn about demographic history and natural selection in humans. This new textbook aims to serve as a gateway to modern human population genetics research for those new to the field. It provides an indispensable resource for students, researchers and practitioners from disparate areas of expertise.

Conservation and the Genomics of Populations

Fred W. Allendorf,W. Chris Funk,Sally N. Aitken,Margaret Byrne,Gordon Luikart
Conservation and the Genomics of Populations Book PDF

Author : Fred W. Allendorf,W. Chris Funk,Sally N. Aitken,Margaret Byrne,Gordon Luikart
Publisher : Oxford University Press
Page : 785 pages
File Size : 46,9 Mb
Release : 2022
Category : Science
ISBN : 9780198856566

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Conservation and the Genomics of Populations by Fred W. Allendorf,W. Chris Funk,Sally N. Aitken,Margaret Byrne,Gordon Luikart Pdf

The relentless loss of biodiversity is among the greatest problems facing the world today. The third edition of this established textbook provides an updated and comprehensive overview of the essential background, concepts, and tools required to understand how genetics can be used to conservespecies, reduce threat of extinction, and manage species of ecological or commercial importance. This edition is thoroughly revised to reflect the major contribution of genomics to conservation of populations and species. It includes two new chapters: "Genetic Monitoring" and a final "ConservationGenetics in Practice" chapter that addresses the role of science and policy in conservation genetics.New genomic techniques and statistical analyses are crucial tools for the conservation geneticist. This accessible and authoritative textbook provides an essential toolkit grounded in population genetics theory, coupled with basic and applied research examples from plants, animals, and microbes. Thebook examines genetic and phenotypic variation in natural populations, the principles and mechanisms of evolutionary change, evolutionary response to anthropogenic change, and applications in conservation and management.Conservation and the Genomics of Populations helps demystify genetics and genomics for conservation practitioners and early career scientists, so that population genetic theory and new genomic data can help raise the bar in conserving biodiversity in the most critical 20 year period in the historyof life on Earth. It is aimed at a global market of applied population geneticists, conservation practitioners, and natural resource managers working for wildlife and habitat management agencies. It will be of particular relevance and use to upper undergraduate and graduate students taking coursesin conservation biology, conservation genetics, and wildlife management.

Population Genomics with R

Emmanuel Paradis
Population Genomics with R Book PDF

Author : Emmanuel Paradis
Publisher : CRC Press
Page : 313 pages
File Size : 49,7 Mb
Release : 2020-03-13
Category : Mathematics
ISBN : 9780429882425

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Population Genomics with R by Emmanuel Paradis Pdf

Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).

Avian Genomics in Ecology and Evolution

Robert H. S. Kraus
Avian Genomics in Ecology and Evolution Book PDF

Author : Robert H. S. Kraus
Publisher : Springer
Page : 348 pages
File Size : 45,6 Mb
Release : 2019-06-29
Category : Science
ISBN : 9783030164775

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Avian Genomics in Ecology and Evolution by Robert H. S. Kraus Pdf

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.

Paleogenomics

Charlotte Lindqvist,Om P. Rajora
Paleogenomics Book PDF

Author : Charlotte Lindqvist,Om P. Rajora
Publisher : Springer
Page : 427 pages
File Size : 46,6 Mb
Release : 2019-01-07
Category : Science
ISBN : 9783030047535

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Paleogenomics by Charlotte Lindqvist,Om P. Rajora Pdf

Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics defines the field of reconstructing and analyzing the genomes of historic or long-dead organisms, most often through comparison with modern representatives of the same or similar species. The opportunity to isolate and study paleogenomes has radically transformed many fields, spanning biology, anthropology, agriculture, and medicine. Examples include understanding evolutionary relationships of extinct species known only from fossils, the domestication of plants and animals, and the evolution and geographical spread of certain pathogens. This pioneering book presents a snapshot view of the history, current status, and future prospects of paleogenomics, taking a broad viewpoint that covers a range of topics and organisms to provide an up-to-date status of the applications, challenges, and promise of the field. This book is intended for a variety of readerships, including upper-level undergraduate and graduate students, professionals and experts in the field, as well as anyone excited by the extraordinary insights that paleogenomics offers.

Population Genetics and Microevolutionary Theory

Alan R. Templeton
Population Genetics and Microevolutionary Theory Book PDF

Author : Alan R. Templeton
Publisher : John Wiley & Sons
Page : 720 pages
File Size : 45,7 Mb
Release : 2006-09-29
Category : Science
ISBN : 9780470047217

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Population Genetics and Microevolutionary Theory by Alan R. Templeton Pdf

The advances made possible by the development of molecular techniques have in recent years revolutionized quantitative genetics and its relevance for population genetics. Population Genetics and Microevolutionary Theory takes a modern approach to population genetics, incorporating modern molecular biology, species-level evolutionary biology, and a thorough acknowledgment of quantitative genetics as the theoretical basis for population genetics. Logically organized into three main sections on population structure and history, genotype-phenotype interactions, and selection/adaptation Extensive use of real examples to illustrate concepts Written in a clear and accessible manner and devoid of complex mathematical equations Includes the author's introduction to background material as well as a conclusion for a handy overview of the field and its modern applications Each chapter ends with a set of review questions and answers Offers helpful general references and Internet links

Molecular Population Genetics

Matthew William Hahn
Molecular Population Genetics Book PDF

Author : Matthew William Hahn
Publisher : Sinauer Associates, Incorporated
Page : 334 pages
File Size : 55,9 Mb
Release : 2018
Category : Molecular genetics
ISBN : 0878939652

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Molecular Population Genetics by Matthew William Hahn Pdf

Published by Sinauer Associates, an imprint of Oxford University Press. Provides descriptions of the methods and tools used in molecular population genetics, which has combined advances in molecular biology and genomics with mathematical and empirical findings to uncover the history of natural selection and demographic shifts in many organisms.

Population Genomics: Microorganisms

Martin F. Polz,Om P. Rajora
Population Genomics Microorganisms Book PDF

Author : Martin F. Polz,Om P. Rajora
Publisher : Springer
Page : 344 pages
File Size : 53,9 Mb
Release : 2019-01-07
Category : Science
ISBN : 9783030047566

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Population Genomics: Microorganisms by Martin F. Polz,Om P. Rajora Pdf

Population genomics is a rapidly emerging field that has the potential to transform our understanding of how evolutionary forces shape genomic diversity among microbes. There have already been considerable advances in understanding gene flow and spread of adaptive traits, and in linking epidemiology with evolutionary biology. The current challenge is to find unifying evolutionary principles for organisms that display a wide range of reproductive biology – from highly clonal to promiscuous – and for which the vast majority have eluded cultivation. This requires interdisciplinary approaches that incorporate novel computational tools, testing of existing and novel population genetic models, and creative new ways of linking genetic diversity to ecological factors. This pioneering book will discuss the advances made and promises of population genomics in microorganisms, outlining some of the key theoretical and practical challenges for microbial population genomics, including defining and identifying populations, genomics-based reverse ecology and building appropriate tools to understand microbes in a variety of complex environments.

A Primer of Molecular Population Genetics

Asher D. Cutter
A Primer of Molecular Population Genetics Book PDF

Author : Asher D. Cutter
Publisher : Oxford University Press, USA
Page : 266 pages
File Size : 44,7 Mb
Release : 2019
Category : Science
ISBN : 9780198838944

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A Primer of Molecular Population Genetics by Asher D. Cutter Pdf

What are the genomic signatures of adaptations in DNA? How often does natural selection dictate changes to DNA? How does the ebb and flow in the abundance of individuals over time get marked onto chromosomes to record genetic history? Molecular population genetics seeks to answer such questions by explaining genetic variation and molecular evolution from micro-evolutionary principles. It provides a way to learn about how evolution works and how it shapes species by incorporating molecular details of DNA as the heritable material. It enables us to understand the logic of how mutations originate, change in abundance in populations, and become fixed as DNA sequence divergence between species. With the revolutionary advances in genomic data acquisition, understanding molecular population genetics is now a fundamental requirement for today's life scientists. These concepts apply in analysis of personal genomics, genome-wide association studies, landscape and conservation genetics, forensics, molecular anthropology, and selection scans. This book introduces, in an accessible way, the bare essentials of the theory and practice of molecular population genetics.

Human Population Genetics and Genomics

Alan R. Templeton
Human Population Genetics and Genomics Book PDF

Author : Alan R. Templeton
Publisher : Academic Press
Page : 498 pages
File Size : 53,8 Mb
Release : 2018-11-08
Category : Science
ISBN : 9780123860262

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Human Population Genetics and Genomics by Alan R. Templeton Pdf

Human Population Genetics and Genomics provides researchers/students with knowledge on population genetics and relevant statistical approaches to help them become more effective users of modern genetic, genomic and statistical tools. In-depth chapters offer thorough discussions of systems of mating, genetic drift, gene flow and subdivided populations, human population history, genotype and phenotype, detecting selection, units and targets of natural selection, adaptation to temporally and spatially variable environments, selection in age-structured populations, and genomics and society. As human genetics and genomics research often employs tools and approaches derived from population genetics, this book helps users understand the basic principles of these tools. In addition, studies often employ statistical approaches and analysis, so an understanding of basic statistical theory is also needed. Comprehensively explains the use of population genetics and genomics in medical applications and research Discusses the relevance of population genetics and genomics to major social issues, including race and the dangers of modern eugenics proposals Provides an overview of how population genetics and genomics helps us understand where we came from as a species and how we evolved into who we are now