Population Genomics: Concepts, Approaches and Applications

Description

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. Front Matter ....Pages i-xvii Front Matter ....Pages 1-1 Population Genomics: Advancing Understanding of Nature (Gordon Luikart, Marty Kardos, Brian K. Hand, Om P. Rajora, Sally N. Aitken, Paul A. Hohenlohe)....Pages 3-79 Front Matter ....Pages 81-81 Genotyping and Sequencing Technologies in Population Genetics and Genomics (J. A. Holliday, E. M. Hallerman, D. C. Haak)....Pages 83-125 Computational Tools for Population Genomics (Jarkko Salojärvi)....Pages 127-160 Population and Evolutionary Genetic Inferences in the Whole-Genome Era: Software Challenges (Alexandros Stamatakis)....Pages 161-175 Front Matter ....Pages 177-177 Population Epigenomics: Advancing Understanding of Phenotypic Plasticity, Acclimation, Adaptation and Diseases (Ehren R. V. Moler, Abdulkadir Abakir, Maria Eleftheriou, Jeremy S. Johnson, Konstantin V. Krutovsky, Lara C. Lewis et al.)....Pages 179-260 Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations (Niko Balkenhol, Rachael Y. Dudaniec, Konstantin V. Krutovsky, Jeremy S. Johnson, David M. Cairns, Gernot Segelbacher et al.)....Pages 261-322 Paleogenomics: Genome-Scale Analysis of Ancient DNA and Population and Evolutionary Genomic Inferences (Tianying Lan, Charlotte Lindqvist)....Pages 323-360 Genome-Wide Association Studies and Heritability Estimation in the Functional Genomics Era (Dunia Pino Del Carpio, Roberto Lozano, Marnin D. Wolfe, Jean-Luc Jannink)....Pages 361-425 Genomic Selection (Elisabeth Jonas, Freddy Fikse, Lars Rönnegård, Elena Flavia Mouresan)....Pages 427-480 Front Matter ....Pages 481-481 Population Genomics Provides Key Insights in Ecology and Evolution (Paul A. Hohenlohe, Brian K. Hand, Kimberly R. Andrews, Gordon Luikart)....Pages 483-510 Inferring Demographic History Using Genomic Data (Jordi Salmona, Rasmus Heller, Martin Lascoux, Aaron Shafer)....Pages 511-537 Advancing Biogeography Through Population Genomics (Jeremy S. Johnson, Konstantin V. Krutovsky, Om P. Rajora, Keith D. Gaddis, David M. Cairns)....Pages 539-585 Adaptation Without Boundaries: Population Genomics in Marine Systems (Marjorie F. Oleksiak)....Pages 587-612 Population Genomics of Speciation and Admixture (Nicola J. Nadeau, Takeshi Kawakami)....Pages 613-653 Population Genomics of Colonization and Invasion (Shana R. Welles, Katrina M. Dlugosch)....Pages 655-683 Population Genomics of Crop Domestication: Current State and Perspectives (Philippe Cubry, Yves Vigouroux)....Pages 685-707 Population Genomics of Animal Domestication and Breed Development (Samantha Wilkinson, Pamela Wiener)....Pages 709-753 Population Genomics of Domestication and Breed Development in Canines in the Context of Cognitive, Social, Behavioral, and Disease Traits (Kristopher J. L. Irizarry, Elton J. R. Vasconcelos)....Pages 755-806 Back Matter ....Pages 807-822