The long-awaited revision of the industry standard on phylogenetics

Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come.

This new edition of "Phylogenetics" captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography--the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics.

The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes:

Parsimony and parsimony analysis

Parametric phylogenetics including maximum likelihood and Bayesian approaches

Phylogenetic classification

Critiques of evolutionary taxonomy, phenetics, and transformed cladistics

Specimen selection, field collecting, and curating

Systematic publication and the rules of nomenclature

Providing a thorough synthesis of the field, this important update to "Phylogenetics" is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.

Genetic Engineering, Volume 25 contains discussions of contemporary and relevant topics in genetics, including:
- Genotyping by Mass Spectrometry;
- Development of Targeted Viral Vectors for Cardiovascular Gene Therapy;
- Practical Applications of Rolling Circle Amplification of DNA Templates;
- Bacterial ION Channels;
- Applications of Plant Antiviral Proteins;
- The Bacterial Scaffoldin: Structure, Function and Potential Applications in the Nanosciences. This principles and methods approach to genetics and genetic engineering is essential reading for all academics, bench scientists, and industry professionals wishing to take advantage of the latest and greatest in this continuously emerging field.

A comprehensive introduction to modern applied statistical genetic data analysis, accessible to those without a background in molecular biology or genetics. Human genetic research is now relevant beyond biology, epidemiology, and the medical sciences, with applications in such fields as psychology, psychiatry, statistics, demography, sociology, and economics. With advances in computing power, the availability of data, and new techniques, it is now possible to integrate large-scale molecular genetic information into research across a broad range of topics. This book offers the first comprehensive introduction to modern applied statistical genetic data analysis that covers theory, data preparation, and analysis of molecular genetic data, with hands-on computer exercises. It is accessible to students and researchers in any empirically oriented medical, biological, or social science discipline; a background in molecular biology or genetics is not required. The book first provides foundations for statistical genetic data analysis, including a survey of fundamental concepts, primers on statistics and human evolution, and an introduction to polygenic scores. It then covers the practicalities of working with genetic data, discussing such topics as analytical challenges and data management. Finally, the book presents applications and advanced topics, including polygenic score and gene-environment interaction applications, Mendelian Randomization and instrumental variables, and ethical issues. The software and data used in the book are freely available and can be found on the book's website.

Genome sequence studies have become more and more important for plant breeding. Brassicas and Legumes: From Genome Structure to Breeding comprises 16 chapters and presents both an overview and the latest results of this rapidly expanding field. Topics covered include: genome analysis of a flowering plant, Arabidopsis thaliana; the sequence of the Arabidopsis genome as a tool for comparative structural genomics in Brassicaceae; application of molecular markers in Brassica coenospecies; the molecular genetic basis of flowering time variation in Brassica species; quantitative trait loci for clubroot resistance in Brassica oleracea; structural differences of S locus between Brassica oleracea and Brassica rapa; Brassica and legume chromosomes; sequence analysis of the Lotus japonicus genome; introduction of an early flowering accession ‘Miyakojima’ MG-20 to molecular genetics in Lotus japonicus; genetic linkage map of the model legume Lotus japonicus; construction of a high quality genome library of Lotus japonicus; genome analysis of Mesorhizobium loti: a symbiotic partner to Lotus japonicus; molecular linkage map of the model legume Medicago truncatula; genetic mapping of seed and nodule protein markers in diploid alfalfa (Medicago sativa); mapping the chickpea (Cicer arietinum) genome: localization of fungal resistance genes in interspecific crosses.  

Ever since Dolly, the Scottish lamb, tottered on wobbly legs into our consciousness-followed swiftly by other animals: first, mice; then pigs that may provide human transplants, and even an ordinary house cat-thoughts have flown to the cloning of human beings. Legislators rushed to propose a ban on a technique that remains highly hypothetical, although some independent researchers have announced their determination to pursue the possibilities. Political scientist and well-known expert on reproductive issues, Andrea L. Bonnicksen examines the political reaction to this new-born science and the efforts to construct cloning policy. She also looks at issues that relate to stem cell research, its even newer sibling, and poses a key question:

How does the response to Dolly guide us as we manage innovative reproductive technologies in the future?

Various legislative endeavors and the efforts by the Food and Drug Administration (FDA) to oversee cloning, as well as policy models related to federal funding, individual state laws, and programs abroad, inform Bonnicksen's identification of four types of cloning policy. She analyzes in depth the roles of diverse interest groups as each struggle to become the dominant voice in the decision-making process. With skill and insight, she clears the mists from a complicated topic, and addresses the legal, political, and ethical arguments that are not likely to disappear from the national conversation or debates any time soon.

Genetic Engineering, Volume 24 contains discussions of contemporary and relevant topics in genetics, including:

-Gene silencing: principles and applications,
-Integrins and the myocardium,
-Plant virus gene vectors: biotechnology and applications in agriculture and medicine,
-Novel approaches to controlling transcription,
-Use of DNA polymorphisms in genetic mapping,
-Application of FLP/FRT site-specific DNA recombination system in plants.
This principles and methods approach to genetics and genetic engineering is essential reading for all academics, bench scientists, and industry professionals wishing to take advantage of the latest and greatest in this continuously emerging field.

th We compiled this volume mostly from presentations at the 6 International Plant Cold Hardiness Seminar (PCHS) after consulting with Professor Tony H. H. Chen, Oregon State University, USA, Professor Pekka Heino, University of Helsinki, Finland, th and Dr. Gareth J. Warren, University of London, Surrey, UK. The 6 International PCHS was held at the Unitas Congress Center, Helsinki, Finland from July 1-5, 2001. There were 110 registered scientists at the serttinar representing 20 countries: Australia, Belgium, Canada, Chile, the Czech Republic, Denmark, Estonia, Finland, Gennany, Hungary, Iceland, Italy, Japan, Norway, Poland, Spain, Sweden, Taiwan, United Kingdom, and United States of America. The infonnation compiled represents the state of the art of research in phmt cold hardiness in tenns of gene regulation, gene expression, signal transduction, the physiology of cold hardiness and, ultimately, the genetic engineering for cold tolerant plants. The International PCHS was initiated in 1977 at the University of Minnesota, St. Paul, Minnesota. It has been traditionally held at 5-year intervals at various locations. th Because of the rapid advances of research in plant cold hardiness, attendees at the 6 meeting unanimously adopted a resolution to hold the seminar in 3-year intervals instead of 5 in the future. Consequently, the next seminar will be held in 2004 in Sapporo, Japan, and Professor Seizo Fujikawa from Hokkaido University will serve as the host.

The debate over genetic manipulation and its use in plant improvement and protection has led to an increased demand for developing methods for detecting and characterizing genetic manipulation in plants and plant products such as seeds and foods. This book is unique in presenting all relevant methods together in one volume: those for using and determining markers retained in genetically manipulated products as well as methods for eliminating marker genes and procedures for characterizing chromosomal aberrations in genetically manipulated plants.

There is an urgent need for guidelines for monitoring of genetically modified higher plants, GMHP. Biotech crops are now cultivated in large scale in North America and elsewhere. In Europe, new genetically modified (GM) products will probably be placed on the market soon and made available of any negative ef for cultivation in the field. Monitoring and surveillance programs for detection fects to the environment must be designed and ready when these crops are released. This also corre sponds to the current intentions made by the European Commission to include monitoring in current biotechnology regulation. Monitoring of changes in biological systems is different from other types of environmental monitoring, such as monitoring fate of chemical pollutants, by focusing primarily on organism survival and organism interactions instead of physical and chemical parameters. The difficulties involved in monitoring biological systems are great, due to the complex interactions between organisms and the variability in responses. Problems concerning spatial and temporal pa rameter variation increase the difficulties, but may be remedied somewhat by the use of "baselines." These and many other questions are discussed in the present book with the aim of presenting practi cal solutions to the needs of GMHP monitoring. A project was initiated in 1998 to produce a book with guidelines for monitoring and surveillance of GMHP. In two earlier books, compilations of current test methods for risk assessment of GMHP were presented (Kjellsson & Simonsen 1994, Kjellsson et al. 1997)."

Once confined to the research laboratory, the genetic engineering of plants is now a big business that is changing the face of modern agriculture. Giant corporations are creating designer crops with strange powers, from cholesterol-reducing soybeans to plants that act as miniature drug factories, churning out everything from vaccines to insulin. They promise great benefits: better health for consumers, more productive agriculture - even an end to world hunger. But the vision has a dark side, one of profit-driven tampering with life and the possible destruction of entire ecosystems. In this text Daniel Charles takes us deep inside research labs, farm sheds and corporate boardrooms to reveal the hidden story behind this agricultural revolution. He tells how a handful of scientists at Monsanto drove biotechnology from the lab into the field, and how the company's opponents are fighting back with every tool available to them, including the cynical manipulation of public fears. A dramatic account of boundless ambition, political intrigue and the quest for knowledge, this is ultimately a story of idealism and of conflicting dreams about the shape of a better world.

The Cyborg Experiments analyzes the challenges posed to corporeality by techology. Taking as their starting point the work of the highly influential performance artists Orlan and Stelarc, the essays in this timely and important collection raise a number of questions in relation to new conceptions of embodiment, identity and otherness in the age of new technologies: Has the body become obsolete? Does transgender challenge traditional ideas of agency? Have we always been cyborgs?In addition to highlighting the playful character of digital aesthetics, the contributors investigate ethical issues concerning the ownership of our bodies and the experiments we perform on them. In this way the book explores how humanism, and ideas of the human, have been placed under increasing scrutiny as a result of new developments in science, media and communications.Contributors:John Appleby, Rachel Armstrong, Fred Botting, Julie Clarke, Gary Hall, Chris Hables Gray, Meredith Jones, Orlan, Mark Poster, Jay Prosser, E. A. Scheer, Zod Sofia, Stelarc, Scott Wilson, Joanna Zylinska.

Changing environmental conditions substantially affect genetic variation and its dynamics in forest ecosystems and various systems of plantations. In response to these challenges, the present book focuses on the response to stress in terms of case studies which address physiological and genetic characters as well as various metric traits. Furthermore a choice of studies is presented which refers to diversity and geographic variation of various species and site conditions, respectively. In addition, genetic resources are characterised and a variety of studies is compiled which address reproduction and migration as well as management aspects. Finally, a set of studies is presented which focus on forest tree breeding with respect to uncertain climatic futures.

Since the late 1990s, few areas of science have been able to compete with genetics when it comes to attracting public interest. The mapping of the entire human gene pool, the Hugo project, makes clear that genetics and gene technology concern life itself. The analysis of the human DNA means that new medicines can be designed, but also that human genetic material can be patented and commercialized. In this volume scholars shed light on the links between biotechnology and economics from a multidisciplinary perspective. Patent on genes, national and global power (im)balance, as well as human and plant genomics, are discussed.

Over the past decade, our laboratory and others have been concerned with molecular archaeological studies aimed at revealing the origins and evolutionary histories of permeases (1). These studies have revealed that several different families, defined on the basis of sequence similarities, arose independently of each other, at different times in evolutionary history, following different routes. When complete microbial genomes first became available for analysis, we adapted p- existing software and designed new programs that allowed us quickly to identify probable transmembrane proteins, estimate their topologies and determine the likelihood that they function in transport (2). This work allowed us to expand previously-recognized families and to identify dozens of new families. All of this work then led us to attempt to design a rational but comprehensive classification system that would be applicable to the complete complement of transport systems found in all living organisms (3). The classification system that we have devised is based primarily on mode of transport and energy coupling mechanism, secondarily on molecular phylogeny, and lastly on the substrate specificities of the individual permeases (4).

As the major task of sequencing the human genome is near completion and full complement of human genes are catalogued, attention will be focused on the ultimate goal: to understand the normal biological functions of these genes, and how alterations lead to disease states. In this task there is a severe limitation in working with human material, but the mouse has been adopted as the favored animal model because of the available genetic resources and the highly conserved gene conservation linkage organization. In just of ten years since the first gene-targeting experiments were p- formed in embryonic stem (ES) cells and mutations transmitted through the mouse germline, more than a thousand mouse strains have been created. These achievements have been made possible by pioneering work that showed that ES cells derived from preimplantation mouse embryos could be cultured for prolonged periods without differentiation in culture, and that homologous rec- bination between targeting constructs and endogenous DNA occurred at a f- quency sufficient for recombinants to be isolated. In the next few years the mouse genome will be systematically altered, and the techniques for achi- ing manipulations are constantly being streamlined and improved.

This volume, as with the previous books in the series, presents state-of-the-art discussions in genetics and genetic engineering by focusing on plant science and technology, agriculture, cell biology, and medical research.

David Fisher, MD, PhD, and an authoritative panel of academic, cutting-edge researchers review and summarize the current state of the field. Describing the broad roles of tumor suppressors from a perspective based in molecular biology and genetics, the authors detail the major suppressors and the pathways they regulate, including cell cycle progression, stress responses, apoptosis, and responses to DNA damage. Leading-edge and forward-looking, Tumor Suppressor Genes in Human Cancer illuminates what is currently known of tumor suppressor genes and their regulation, work that is already beginning to revolutionize cancer target elucidation, drug discovery, and treatment design.

During the past five to ten years, a variety of tools has been developed in the disciplines of both gene engineering, and molecular and structural biology. Some of these advances have permitted scientists not only to identify and characterize genes, but also to target these genes by disruption, thus eliminating their function in living animals, and to det- mine the biological responses to altered gene products. This has particular significance in endocrine systems, in which feedback mechanisms between the hypothalamus, pi- itary, and end organs are critical in normal physiology. Interpretation of the physiological significance, or the site of action of specific molecules in this context, has been difficult prior to transgenic technology. Major advances have occurred specifically in the areas of growth and development, and of reproduction. Coupled with analysis of naturally occurring mutations in humans, the use of transgenic animals and in vitro systems has recently allowed endocrinologists to understand the importance of specific thyroid hormone receptor isoforms in vivo, the molecular basis for generalized resistance to thyroid hormones via mutations in the nuclear receptor, and mechanisms for suppressing gene transcription. Previously designated "orphan rec- tors," such as steroidogenic factor-1, were demonstrated to have critical roles in dev- opment and reproduction. Other nuclear receptors-including those for thyroid hormone, estrogens, androgens, and progesterone-were shown to bind to coactivator and co- pressor proteins that modified their transcriptional activity, and contributed to the ce- specific effects of the hormones.

As access to genetic technology increases, patients, ethicists, physicians and policy makers are forced to make quick case decisions on uncharted ethical ground. In Genetic Dilemmas Davis seeks to give us an understanding of the options and consequences of these new genetic "choices". Issues addressed include: disabled parents who seek assistance in conceiving a child who shares their disability; genetic testing of children with no immediate medical benefit; sex selection and determination of foetal sex; and the cloning of human beings.

The potential now exists in many experimental systems to transfer a cloned, modified gene back into the genome of the host organism. In the ideal situation, the cloned gene is returned to its homologous location in the genome and becomes inserted at the target locus. This process is a controlled means for the repair of DNA damage and ensures accurate chromosome disjunction during meiosis. The paradigm for thinking about the mechanism of this p- cess has emerged primarily from two sources: (1) The principles of reaction mechanics have come from detailed biochemical analyses of the RecA protein purified from Escherichia coli; and (2) the principles of information transfer have been derived from genetic studies carried out in bacteriophage and fungi. A compelling picture of the process of homologous pairing and DNA strand exchange has been influential in directing investigators interested in gene t- geting experiments. The ability to find and pair homologous DNA molecules enables ac- rate gene targeting and is the central phenomenon underlying genetic recombi- tion. Biochemically, the overall process can be thought of as a series of steps in a reaction pathway whereby DNA molecules are brought into homologous register, the four-stranded Holliday structure intermediate is formed, hete- duplex DNA is extended, and DNA strands are exchanged. Not much is known about the biochemical pathway leading to homologous recombination in euka- otes.

This volume reviews the latest research on using genetically engineered plants and plant viruses to produce new products for medicine and industry. Individual chapters cover the three main technologies for engineering plants: Agrobacterium-mediated transformation; particle bombardment transformation; and plant viral vectors. Additional chapters deal with strategies for producing medically important products such as vaccines, human enzymes, monoclonal antibodies, and other therapeutic proteins in plants. In addition to presenting up-to-date reviews of current research efforts, the book also contains some thoughtful discussions on the potential benefits and risks involved in producing pharmaceuticals in plants and the challenges of bringing such products to market.

Aspects of genetic engineering research emphasized in this volume are applications to plants (crop plants and grass, both important for human needs) and new methodologies, such as Tar cloning, which make it much easier to isolate specific regions from complex genomes. Another subject discussed is linear DNA replication of prokaryotes.

In Human Cloning a panel of distinguished philosophers, medical ethicists, religious thinkers, and social critics tackle the thorny problems raised by the now real possibility of human cloning. In their wide ranging reviews, the distinguished contributors critically examine the major arguments for and against human cloning, probe the implications of such a procedure for society, and critically evaluate the "Report and Recommendations of the National Bioethics Advisory Commission." The debate includes both religious and secular arguments, as well as an outline of the history of the cloning debate and a discussion of human cloning's impact on our sense of self and our beliefs about the meaning of life.

Presents the latest research in genetic engineering. Topics include agrobacterium -mediated horizontal gene transfer, detection of single nucleotide variations, the ribosome as a vehicle for antisense RNA, cloning and expression of large mammalian cDNAs, the use of genetically engineered cells in dr

These Proceedings evolved from the OECD Co-operative Research Programme workshop on "Potential ecological impact of transgenic plants expressing viral sequencies," held at the Agricultural Biotechnology Center in Godollo, Hungary on 24-26 April 1997. The OECD Co-operative Research Programme At the Directorate for Agrieulture of the Organisation for Economie Co-operation and Development (OECD) a co-operative research programme for "Biological Resource Management" has existed since 1990. It foeuses on work in four specific topie areas, one of whieh is "Ecology and utilisation of new organisms" (Theme 3). The activities promoted by this programme are post-doctoral fellowships (announced annually), and the organisation of expert workshops (1-2 workshops per Theme per year). The 26 OECD member countries participating in this programme are: Australia, Austria, Belgium, Canada, Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Ireland, ltaly, Korea, Japan, the NetherIands, New Zealand, Norway, Poland, Portugal, Spain, Sweden, SwitzerIand, Turkey, the UK, and the USA."