Population Genomics With R

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 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 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.

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

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

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 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.

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.