Population Genomics With R

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Population Genomics with R

Emmanuel Paradis
Population Genomics with R Book PDF

Author : Emmanuel Paradis
Publisher : CRC Press
Page : 378 pages
File Size : 42,6 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).

Population Genomics with R

Emmanuel Paradis
Population Genomics with R Book PDF

Author : Emmanuel Paradis
Publisher : CRC Press
Page : 313 pages
File Size : 51,7 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).

Population Genetics with R

Áki Jarl Láruson,Floyd Allan Reed
Population Genetics with R Book PDF

Author : Áki Jarl Láruson,Floyd Allan Reed
Publisher : Oxford University Press, USA
Page : 218 pages
File Size : 49,7 Mb
Release : 2021-02-25
Category : Computers
ISBN : 9780198829539

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Population Genetics with R by Áki Jarl Láruson,Floyd Allan Reed Pdf

This book focuses on applying the hugely popular R software specifically to the field, offering an accessible, step-by-step guide to tackling the challenges of achieving effective data interpretation and summary.

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 : 51,8 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

Population Genomics

Om P. Rajora
Population Genomics Book PDF

Author : Om P. Rajora
Publisher : Springer
Page : 822 pages
File Size : 43,7 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.

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 : 51,5 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 : 40,7 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 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 : 51,6 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

Population Genetics with R

Áki Jarl Láruson,Floyd Allan Reed
Population Genetics with R Book PDF

Author : Áki Jarl Láruson,Floyd Allan Reed
Publisher : Oxford University Press
Page : 256 pages
File Size : 42,9 Mb
Release : 2021-02-24
Category : Science
ISBN : 9780192565037

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Population Genetics with R by Áki Jarl Láruson,Floyd Allan Reed Pdf

Population genetics is an inherently quantitative discipline, yet often focuses upon abstract concepts which can be difficult to conceptualize and appropriately visualize at first glance. This book focuses on applying the hugely popular R software specifically to the field, offering an accessible, step-by-step guide to tackling the challenges of achieving effective data interpretation and summary. The authors adopt an engaging "learning by doing" approach that will enable readers to develop an intuitive understanding of key population genetics concepts through the use of R. Beginning with the groundwork of installing and using R (including CRAN and the RStudio IDE), the book works through the use of basic commands for data manipulation. An introduction to basic terminology in population genetics follows, clearly explaining how these fundamental assumptions can provide insights and form basic inferences for real populations. The focus then moves onto statistical tests including writing and running algorithms as functions. Subsequent chapters examine genetic variation, adaptation, and natural selection as well as different approaches to population differences. Importantly, the accompanying set of practical exercises demonstrate that implementing all of these concepts via programming can actually help greatly in understanding them, even if they may at first seem insurmountably complex. Finally, this accessible textbook points the way forwards to other key concepts that are important to understanding modern day population genetics research (in particular coalescent theory) and offers the reader useful launching points for further learning. Population Genetics with R is aimed at students ranging from undergraduate to postgraduate level in the fields of population genetics, ecology, evolutionary biology, conservation genetics, computational biology, and biostatistics.

Statistical Population Genomics

Julien Y Dutheil
Statistical Population Genomics Book PDF

Author : Julien Y Dutheil
Publisher : Unknown
Page : 464 pages
File Size : 42,8 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.

Handbook of Statistical Genomics

David J. Balding,Ida Moltke,John Marioni
Handbook of Statistical Genomics Book PDF

Author : David J. Balding,Ida Moltke,John Marioni
Publisher : John Wiley & Sons
Page : 1828 pages
File Size : 53,5 Mb
Release : 2019-07-09
Category : Science
ISBN : 9781119429258

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Handbook of Statistical Genomics by David J. Balding,Ida Moltke,John Marioni Pdf

A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.

Introduction to Genomics

Arthur Lesk
Introduction to Genomics Book PDF

Author : Arthur Lesk
Publisher : Oxford University Press
Page : 421 pages
File Size : 44,6 Mb
Release : 2012
Category : Medical
ISBN : 9780199564354

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Introduction to Genomics by Arthur Lesk Pdf

This book covers the latest techniques that enable us to study the genome in detail, the book explores what the genome tells us about life at the level of the molecule, the cell, and the organism

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 : 40,5 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.

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 : 49,9 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.

Applied Statistical Genetics with R

Andrea S. Foulkes
Applied Statistical Genetics with R Book PDF

Author : Andrea S. Foulkes
Publisher : Springer Science & Business Media
Page : 264 pages
File Size : 52,7 Mb
Release : 2009-04-28
Category : Science
ISBN : 9780387895543

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Applied Statistical Genetics with R by Andrea S. Foulkes Pdf

Statistical genetics has become a core course in many graduate programs in public health and medicine. This book presents fundamental concepts and principles in this emerging field at a level that is accessible to students and researchers with a first course in biostatistics. Extensive examples are provided using publicly available data and the open source, statistical computing environment, R.