Dramatic advances in computing power enable simulation of DNA sequences generated by complex microevolutionary scenarios that include mutation, population structure, natural selection, meiotic recombination, demographic change, and explicit spatial geographies. Although retrospective, coalescent simulation is computationally efficient-and covered here-the primary focus of this book is forward-in-time simulation, which frees us to simulate a wider variety of realistic microevolutionary models. The book walks the reader through the development of a forward-in-time evolutionary simulator dubbed FORward Time simUlatioN Application (FORTUNA). The capacity of FORTUNA grows with each chapter through the addition of a new evolutionary factor to its code. Each chapter also reviews the relevant theory and links simulation results to key evolutionary insights. The book addresses visualization of results through development of R code and reference to more than 100 figures. All code discussed in the book is freely available, which the reader may use directly or modify to better suit his or her own research needs. Advanced undergraduate students, graduate students, and professional researchers will all benefit from this introduction to the increasingly important skill of population genetic simulation.

Somatic genome manipulation is required when a sexual crossing approach cannot be used in breeding or genetic treatment of an individual organism. Examples can include gene- or cell-therapy of a person to correct disease, genetic improvement of vegetatively propagated plants, and genetic replacement of cytoplasm without significantly modifying the nuclear genome. The advantage of somatic genome manipulation is maintenance of the general genotype while correcting one or more traits. Somatic genome manipulation is also an option for genetic improvement of sexually propagated plants in polyploidy breeding or in overcoming issues of sexual incompatibility. Recent novel technologies in somatic genome manipulation are developing quickly but much of this literature is fragmented and difficult or inconvenient to access. This book represents the first attempt to assemble updated reviews, detailed protocols, and their applications in all fields in which somatic genome manipulation has thrived. This is a truely one-of-a-kind work that brings together the most important and relevant advances in somatic genome manipulation in plants, algae, microorganisms, humans and animals, and demonstrates where the science interacts and where it diverges. The chapters are written by experts on the topic with ready-to-use protocols that were originally developed or adapted from the literature in their laboratories. We expect that this book will be useful for students, researchers, and teachers in both plant and animal research as a resource for the latest information on somatic genome manipulation and for its useful laboratory methods.

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.

This book examines the biology of tuco-tucos (Ctenomys) from an evolutionary perspective. Historically, these subterranean rodents have long attracted the attention of scientists due to its remarkable chromosomes variability and rapid diversification. A wealth of knowledge on physiology, ecology, genetics, morphology, paleontology, and taxonomy has been documented in the last 70 years through numerous single publications. In this volume, expert investigators review and frame these essays with the breadth of current understanding. The collection of chapters are presented into the major topics: i) Evolution of Ctenomys, ii) Geographic Patterns, iii) Organismal Biology, and iv) Environmental Relationships. Given its scope, the book will be of interest to both students and researchers and may stimulate further research with this exciting model on a wide range of evolutionary topics.

This book aims to be a comprehensive review of the literature on the conservation genetics of the New World crocodilians, from the biological and demographical aspects of the living species to the application of molecular techniques for conservation purposes. It covers the current status of the molecular genetics applied to phylogenetics, phylogeography, diversity, kinship and mating system, and hybridization, as well its implications for decision making with regards to the conservation of these species at academic and governmental levels. This book can be used as a guide for graduate and undergraduate students to understand how conservation genetics techniques are carried out and how they can help preserve not only crocodilians but also other living species.

This book presents a comprehensive overview of DNA barcoding and molecular phylogeny, along with a number of case studies. It discusses a number of areas where DNA barcoding can be applied, such as clinical microbiology, especially in relation to infection management; DNA database management; and plant -animal interactions, and also presents valuable information on the DNA barcoding and molecular phylogeny of microbes, algae, elasmobranchs, fishes, birds and ruminant mammals. Furthermore it features unique case studies describing DNA barcoding of reptiles dwelling in Saudi Arabian deserts, genetic variation studies in both wild and hatchery populations of Anabas testudineus, DNA barcoding and molecular phylogeny of Ichthyoplankton and juvenile fishes of Kuantan River in Malaysia, and barcoding and molecular phylogenetic analysis of indigenous bacteria from fishes dwelling in a tropical tidal river. Moreover, since prompt identification and management of invasive species is vital to prevent economic and ecological loss, the book includes a chapter on DNA barcoding of invasive species. Given its scope, this book will appeal not only to researchers, teachers and students around the globe, but also to general readers.

This book is a compilation of recent global measures to conserve bio-resources and manage biotic and abiotic stresses. It highlights emerging issues related to agriculture, abiotic and biotic stress factors, ethnic knowledge, climate change and global warming, as well as natural resources and their sustainable management. It also focuses on the consolidated efforts of scientists and academics engaged in addressing a number of issues related to resource management and combating stresses in order to protect the Earth. Crop production and productivity have been significantly improved, however, there have been no corresponding practical advances in sustainable agriculture.This book offers a wide range of affordable approaches to managing bio-resources with a focus on sustainability. Lastly, it describes research highlights and future areas of research.

This book is about the philosophy of de-extinction. To make an extinct species 'de-extinct' is to resurrect it by creating new organisms of the same, or similar, appearance and genetics. The book describes current attempts to resurrect three species, the aurochs, woolly mammoth and passenger pigeon. It then investigates two major philosophical questions such projects throw up. These are the Authenticity Question-'will the products of de-extinction be authentic members of the original species?'-and the Ethical Question-'is de-extinction something that should be done?' The book surveys and critically evaluates a raft of arguments for and against the authenticity or de-extinct organisms, and for and against the ethical legitimacy of de-extinction. It concludes, first, that authentic de-extinctions are actually possible, and second, that de-extinction can potentially be ethically legitimate, especially when deployed as part of a 'freeze now and resurrect later' conservation strategy.

This book presents a concept for implementing a mass balance approach toward developing an effective eco-friendly, livestock farming system independent of external energy input. In this context it describes a modern, integrated farming system, and includes comprehensive technical information explaining the design and evaluation of manure management systems, and modeling and operational tools. It first discusses the mass balance operating process, highlighting the difference between imported and exported mass across the farm boundary. Estimating mass balance can provide critical information for (comprehensive) nutrient management planning and for managing the movement of nutrients and manure. It then explains the estimation of whole-farm P mass balance using a suitable model system. The subsequent chapters provide updated information on management aspects of livestock-farming and generation of multiple job opportunities, and also explore various aspects of livestock farming operational protocols like housing and management; nurture of rams, ewes and lambs, new born calves and heifers; care of buck, doe and kid- nutrition flushing; concept zero grazing-systems; disease control and management; integrated goat farming; and crop-livestock integration. Further, the book addresses crop-livestock integration; energy autonomy in cattle farming; value added biopharmaceuticals from cattle farming; CAPEX for cattle farming; concepts of cattle farming; detrimental effects of the industry; topographic and edaphic factors, and thermal stress on livestock growth and development; socioeconomic development; and water requirements for livestock. The book concludes with the most important issue in the field of agriculture and veterinary science: "Livestock Farming with Care," describing sustainable, eco-friendly livestock farming by highlighting issues like animal feed vs. human food; agricultural GDP vs livestock, and factors affecting the sustainability of livestock farming. Given its scope, this book is a valuable resource for researchers and students alike, and will also appeal to practitioners in the field of livestock.

Drosophila melanogaster (fruit fly) is a highly versatile model with a genetic legacy of more than a century. It provides powerful genetic, cellular, biochemical and molecular biology tools to address many questions extending from basic biology to human diseases. One of the most important questions in biology is how a multi-cellular organism develops from a single-celled embryo. The discovery of the genes responsible for pattern formation has helped refine this question and has led to other questions, such as the role of various genetic and cell biological pathways in regulating the process of pattern formation and growth during organogenesis. The Drosophila eye model has been extensively used to study molecular genetic mechanisms involved in patterning and growth. Since the genetic machinery involved in the Drosophila eye is similar to humans, it has been used to model human diseases and homology to eyes in other taxa. This updated second edition covers current progress in the study of molecular genetic mechanisms of pattern formation, mutations in axial patterning, genetic regulation of growth, and more using the Drosophila eye as a model.

This book examines how biotechnology can improve livestock breeding and farming, and thereby also animal products. In the first chapters the reader will discover which techniques and approaches are currently used to improve animal breeding, animal health and the value of animal products. Particular attention is given to reproduction techniques, animal nutrition and livestock vaccines that not only enhance animal health but also have a significant effect on human health by ensuring safe food procurement and preventing zoonotic diseases. In addition, modern biotechnology can increase not only productivity but also the consistency and quality of animal food, fiber and medical products. In the second part of the book, issues such as how animal biotechnology could affect the environment and the important topic of animal waste management are explored. In the concluding chapter, the authors discuss future challenges related to animal biotechnology. This work will appeal to a wide readership, from scientists and professionals working in animal production, to those in farm animal management and veterinary science.

This book explains omics at the most basic level, including how this new concept can be properly utilized in molecular and systems biology research. Most reviews and books on this topic have mainly focused on the technicalities and complexity of each omics' platform, impeding readers to wholly understand its fundamentals and applications. This book tackles such gap and will be most beneficial to novice in this area, university students and even researchers. Basic workflow and practical guidance in each omics are also described, such that scientists can properly design their experimentation effectively. Furthermore, how each omics platform has been conducted in our institute (INBIOSIS) is also detailed, a comprehensive example on this topic to further enhance readers' understanding. The contributors of each chapter have utilized the platforms in various manner within their own research and beyond. The contributors have also been interactively integrated and combined these different omics approaches in their research, being able to systematically write each chapter with the conscious knowledge of other inter-relating topics of omics. The potential readers and audience of this book can come from undergraduate and postgraduate students who wish to extend their comprehension in the topics of molecular biology and big data analysis using omics platforms. Furthermore, researchers and scientists whom may have expertise in basic molecular biology can extend their experimentation using the omics technologies and workflow outlined in this book, benefiting their research in the long run.

This book, written by experienced geneticists, covers topics ranging from the natural history of the mouse species, its handling and reproduction in the laboratory, and its classical genetics and cytogenetics, to modern issues including the analysis of the transcriptome, the parental imprinting and X-chromosome inactivation. The strategies for creating all sorts of mutations, either by genetic engineering or by using mutagens, are also reviewed and discussed in detail. Finally, a last chapter outlines the methodology used for the analysis of complex or quantitative traits. The authors also discuss the importance of accurate phenotyping, which is now performed in the mouse clinics established worldwide and identify the limits of the mouse model, which under certain circumstances can fail to present the phenotype expected from the cognate condition in the human model. For each chapter an up-to-date list of pertinent references is provided. In short, this book offers an essential resource for all scientists who use or plan to use mice in their research.

Kisspeptin has been shown to be both necessary and sufficient for activation of the reproductive axis, during puberty and later in adulthood. This makes kisspeptin a fundamental component of the reproductive axis. Kisspeptin has been deemed the single most potent stimulator of GnRH neurons yet known. The importance of kisspeptin has been documented in humans as well as non-human animal models, ranging from monkeys, sheep, and rodents to numerous fish species, thus signifying a highly conserved nature of its reproductive function. Importantly, kisspeptin neurons seem to mediate many of the regulatory effects of other signals, whether they are metabolic, circadian, hormonal, or stress. This places kisspeptin neurons in a unique position to be key nodal points and conduits for conveying numerous endogenous and exogenous signals to the reproductive axis.

In Mouse Molecular Embryology: Methods and Protocols, expert researchers in the field detail many of the protocols used to study mouse embryology. These include protocols and techniques that are "close to the embryo": such as, manipulating embryonic gene expression, culturing explanted embryonic tissue and harvesting embryonic RNA. With additional chapters on fluorescence imaging, lineage tracing, and genetic ablation. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Mouse Molecular Embryology: Methods and Protocols seeks to aid scientist in the further study of mouse embryo and its relation to other aspects of biological research.

This laboratory manual, published in cooperation with the International Society for Transgenic Technology (ISTT), provides almost all current methods that can be applied to the creation and analysis of genetically modified animals. The chapters have been contributed by leading scientists who are actively using the technology in their laboratories. Based on their first-hand experience the authors also provide helpful notes and troubleshooting sections. Topics range from standard techniques, such as pronuclear microinjection of DNA, to more sophisticated and modern methods, such as the derivation and establishment of embryonic stem (ES) cell lines, with defined inhibitors in cell culture medium. In addition, related topics with relevance to the field are addressed, including global web-based resources, legal issues, colony management, shipment of mice and embryos, and the three R s: refinement, reduction and replacement.

This is a reference handbook for young researchers exploring gene and cell therapy. Gene therapy could be defined as a set of strategies modifying gene expression or correcting mutant/defective genes through the administration of DNA (or RNA) to cells, in order to treat disease. Important advances like the discovery of RNA interference, the completion of the Human Genome project or the development of induced pluripotent stem cells (iPSc) and the basics of gene therapy are covered. This is a great book for students, teachers, biomedical researchers delving into gene/cell therapy or researchers borrowing skills from this scientific field.

Fluorescence in situ Hybridization (FISH) belongs to that special category of well-established molecular biology techniques that, since their inception a few decades ago, have succeeded in keeping a prominent position within the constantly expanding list of laboratory pro- dures for biomedical research and clinical diagnostics. The design simplicity and cost-effectiveness of the early FISH protocols, combined with the signifcant acceleration of discoveries in related technical areas such as fuor- cence microscopy, digital imaging, and nucleic acid technology have prompted the div- sifcation of the original technique into an outstanding number of imaginative and useful applications, and thus have not only held back its outmoding but have also promoted its expansion into different areas of basic and applied research in the post-genomic era. The 34 chapters included in this book aim at portraying the vibrant complexity and diversity of the current FISH protocol landscape, providing cutting-edge examples of va- ous applications for genetic and developmental research, cancer research, reproductive medicine, diagnostic and prognostic purposes, microbial ecology, and evolutionary st- ies. The book is divided in four parts: (I) Core Techniques, (II) Technical Advancements and Novel Adaptations, (III) Translational FISH: Applications for Human Genetics and Medicine, and (IV) Protocols for Model Organisms.

Progestins play a key role in reproductive endocrinology and as pharmaceutical drugs for contraception and in combined hormone therapy. To further our understanding of progestin action in the mammary gland, an international symposium, attended by leading researchers from academia and industry, was held in Berlin, 21 23 March 2007. Genetic mouse models helped to elucidate the role of progestins, both in normal breast development and in disease. Mechanistic molecular studies inspired the design of new progestins with improved tissue selectivity. In addition, the clinical impact of progesterone receptor agonists and antagonists for the prevention and treatment of breast cancer was discussed.

This volume provides a comprehensive selection of recent studies addressing insect hearing and acoustic communication. The variety of signalling behaviours and hearing organs makes insects highly suitable animals for exploring and analysing signal generation and hearing in the context of neural processing, ecology, evolution and genetics. Across a variety of hearing species like moths, crickets, bush-crickets, grasshoppers, cicadas and flies, the leading researchers in the field cover recent scientific progress and address key points in current research, such as:

. How can we approach the evolution of hearing in insects and what is the developmental and neural origin of the auditory organs?

. How are hearing and sound production embedded in the natural lifestyle of the animals, allowing intraspecific communication but also predator avoidance and even predation?

. What are the functional properties of hearing organs and how are they achieved at the molecular, biophysical and neural levels?

. What are the neural mechanisms of central auditory processing and signal generation?

The book is intended for students and researchers both inside and outside of the fascinating field of bioacoustics and aims to foster understanding of hearing and acoustic communication in insects."

The generation of genetically modified mice is absolutely crucial to gene function studies today, primarily because mice are genetically similar to man and because gene function studies in mice are in the context of a whole organism, making them particularly useful. In Transgenic Mouse Methods and Protocols, Second Edition, expert research explore current advances in the field through detailed laboratory protocols. Chapters provide a general introduction outlining how to deal with mice and how to generate transgenic mouse models, explore the generation of conditional and induced knockout and transgenic mice, and offer alternative routes to studying gene function in mice. Composed in the highly successful Methods in Molecular Biology (TM) series format, each chapter contains a brief introduction, step-by-step methods, a list of necessary materials, and a Notes section which shares tips on troubleshooting and avoiding known pitfalls. Comprehensive and state of the art, Transgenic Mouse Methods and Protocols, second Edition is the ideal guide for all researchers interested in the latest information about the production and analysis of transgenic and knockout mice.

This book provides insight into the instances in which wildlife species can create problems. Some species trigger problems for human activities, but many others need humans to save them and to continue to exist. The text addresses issues faced by economists and politicians dealing with laws involving actions undertaken to resolve the problems of the interaction between humans and wildlife. Here, the words 'problematic species' are used in their broadest sense, as may be appreciated in the short introductions to the various sections. At times, the authors discuss special cases while always extending the discussion into a more general and broad vision. At others, they present real cutting-edge analysis of ecological topics and issues. The book will be of interest to biologists, ecologists and wildlife managers involved in research on wildlife, parks, and environmental management, as well as to government departments and agencies, NGOs and conservation wildlife organizations. Even those in contact with nature, such as hunters, herders, and farmers, will be able to find a great deal of important information. Specific case studies are selected from among the most significant and prevalent cases throughout the world. A total of 26 papers have been selected for this book, written by zoologists, biologists and ecologists. Many have an interdisciplinary approach, with contributions by economists, criminologists, technical specialists, and engineers.

The aim of this book is to systematize and discuss population genetic studies of freshwater fish in a region that harbors the greatest diversity of species among all inland water ecosystems. This volume explores the genetic evaluation for a number of orders, families and species of Neotropical fishes, and provides an overview on genetic resources and diversity and their relationships with fish domestication, breeding, and food production.