Gene regulation is tightly regulated to produce individual phenotypes appropriate to a animal's placement in time and space. How specific genetic and environmental factors shape gene regulation has been extensively studied in laboratory model species. However, far less is known about sources of variance in gene regulation in the wild, in populations where natural selection operates. My dissertation research aimed to identify factors that influence individual variation in gene regulation by evaluating transcriptome-wide gene expression levels within and across populations. In my first chapter, I evaluated gene expression changes in captive Swainson's thrushes (Catharus ustulatus) originating from two populations as they transitioned from the non-migratory to migratory condition. Birds exhibited significant seasonal differences in the expression of genes involved in cellular development in the brain, providing support for seasonal neural plasticity in migratory birds. In my second chapter, I focused on a single population, the North American gray wolves (Canis lupus) of Yellowstone National Park, to evaluate the relative impacts of intrinsic (age and sex) and environmental variables (social status and presence of sarcoptic mange) on gene expression variation in blood. I found that, unexpectedly, animal age, but not sex, social status, or sarcoptic mange infestation, impacted gene expression, suggesting that age may have pervasive, evolutionarily conserved effects on gene expression variation in natural populations of mammals. Finally, in my third chapter, I adopted an in vitro experimental approach to study how gene regulation is impacted by genotype at the CBD103 gene, which encodes a protein with antimicrobial properties, exists in two forms (alleles) in North American gray wolves, and is associated with lifetime reproductive success. I established keratinocyte lines from 24 gray wolves and utilized CRISPR/Cas9 to generate one heterozygous and homozygous line. To test whether the fitness effects of CBD103 genotype are explained by their roles in immune defense, I challenged the cells with synthetic antigens and live canine distemper virus. No effect of CBD103 genotype was detected, but immune challenge altered expression of thousands of genes. This work demonstrated the ability to establish a population panel of cell lines from a wild mammal, a potentially powerful method for studying gene regulation in natural populations.

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.

Conservation genetics focuses on understanding the role and requirement of genetic variation for population persistence. However, considerable debate now surrounds the role of genetic factors (as opposed to non-genetic factors such as habitat destruction etc.) in population extinction, and a comprehensive synthesis is now timely. Can extinction be explained by habitat destruction alone or is lack of genetic variation a part of the explanation? The book thoroughly reviews the arguments for a role of genetics in the present biodiversity crisis. It describes the methods used to study genetic variation in endangered species and examines the influence of genetic variation in the extinction of species. To date, conservation genetics has predominantly utilized neutral genetic markers e.g. microsatellites. However, with the recent advances in molecular genetics and genomics it will soon be possible to study 'direct gene action', following the fate of genetic variation at the level of DNA, through expression, to proteins in order to determine how such phenotypes fare in populations of free living organisms. Evolutionary Conservation Genetics explores these exciting avenues of future research potential, integrating ecological quantitative genetics with the new genome science. It is now more important than ever that we ask relevant questions about the evolutionary fate of endangered populations throughout the globe and incorporate our knowledge of evolutionary processes and the distribution of genetic diversity into effective conservation planning and action.

Gene expression is the most fundamental level at which genotype gives rise to phenotype, which is an obvious, observable, and measurable trait. Phenotype is dependent on genetic makeup of the organism and influenced by environmental conditions. This book explores the significance, mechanism, function, characteristic, determination, and application of gene expression and phenotypic traits.

The average person can name more bird species than they think, but do we really know what a bird “species” is? This open access book takes up several fascinating aspects of bird life to elucidate this basic concept in biology. From genetic and physiological basics to the phenomena of bird song and bird migration, it analyzes various interactions of birds – with their environment and other birds. Lastly, it shows imminent threats to birds in the Anthropocene, the era of global human impact. Although it seemed to be easy to define bird species, the advent of modern methods has challenged species definition and led to a multidisciplinary approach to classifying birds. One outstanding new toolbox comes with the more and more reasonably priced acquisition of whole-genome sequences that allow causative analyses of how bird species diversify. Speciation has reached a final stage when daughter species are reproductively isolated, but this stage is not easily detectable from the phenotype we observe. Culturally transmitted traits such as bird song seem to speed up speciation processes, while another behavioral trait, migration, helps birds to find food resources, and also coincides with higher chances of reaching new, inhabitable areas. In general, distribution is a major key to understanding speciation in birds. Examples of ecological speciation can be found in birds, and the constant interaction of birds with their biotic environment also contributes to evolutionary changes. In the Anthropocene, birds are confronted with rapid changes that are highly threatening for some species. Climate change forces birds to move their ranges, but may also disrupt well-established interactions between climate, vegetation, and food sources. This book brings together various disciplines involved in observing bird species come into existence, modify, and vanish. It is a rich resource for bird enthusiasts who want to understand various processes at the cutting edge of current research in more detail. At the same time it offers students the opportunity to see primarily unconnected, but booming big-data approaches such as genomics and biogeography meet in a topic of broad interest. Lastly, the book enables conservationists to better understand the uncertainties surrounding “species” as entities of protection.

Advances in Animal Genomics provides an outstanding collection of integrated strategies involving traditional and modern - omics (structural, functional, comparative and epigenomics) approaches and genomics-assisted breeding methods which animal biotechnologists can utilize to dissect and decode the molecular and gene regulatory networks involved in the complex quantitative yield and stress tolerance traits in livestock. Written by international experts on animal genomics, this book explores the recent advances in high-throughput, next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches which have enabled to produce huge genomic and transcriptomic resources globally on a genome-wide scale. This book is an important resource for researchers, students, educators and professionals in agriculture, veterinary and biotechnology sciences that enables them to solve problems regarding sustainable development with the help of current innovative biotechnologies. Integrates basic and advanced concepts of animal biotechnology and presents future developments Describes current high-throughput next-generation whole genome and transcriptome sequencing, array-based genotyping, and modern bioinformatics approaches for sustainable livestock production Illustrates integrated strategies to dissect and decode the molecular and gene regulatory networks involved in complex quantitative yield and stress tolerance traits in livestock Ensures readers will gain a strong grasp of biotechnology for sustainable livestock production with its well-illustrated discussion

Whereas genetic studies have traditionally focused on explaining heritance of single traits and their phenotypes, recent technological advances have made it possible to comprehensively dissect the genetic architecture of complex traits and quantify how genes interact to shape phenotypes. This exciting new area has been termed systems genetics and is born out of a synthesis of multiple fields, integrating a range of approaches and exploiting our increased ability to obtain quantitative and detailed measurements on a broad spectrum of phenotypes. Gathering the contributions of leading scientists, both computational and experimental, this book shows how experimental perturbations can help us to understand the link between genotype and phenotype. A snapshot of current research activity and state-of-the-art approaches to systems genetics are provided, including work from model organisms such as Saccharomyces cerevisiae and Drosophila melanogaster, as well as from human studies.