Evolving Pathways

Evolutionary developmental biology, or 'evo-devo', is the study of the relationship between evolution and development. Dealing specifically with the generative mechanisms of organismal form, evo-devo goes straight to the core of the developmental origin of variation, the raw material on which natural selection (and random drift) can work. Evolving Pathways brings together contributions that represent a diversity of approaches. Topics range from developmental genetics to comparative morphology of animals and plants alike, and also include botany and palaeontology, two disciplines for which the potential to be examined from an evo-devo perspective has largely been ignored until now. Researchers and graduate students will find this book a valuable overview of current research as we begin to fill a major gap in our perception of evolutionary change.

The evolution of metazoans has been accompanied by new interfaces with the microbial environment that include biological barriers and surveillance by specialized cell types. Increasingly complex organisms require increased capacities to confront pathogens, achieved by co-evolution of recognition mechanisms and regulatory pathways. Two distinct but interactive forms of immunity have evolved. Innate immunity, shared by all metazoans, is traditionally viewed as simple and non-specific. Adaptive immunity possesses the capacity to anticipate new infectious challenges and recall previous exposures; the most well-understood example of such a system, exhibited by lymphocytes of vertebrates, is based on somatic gene alterations that generate extraordinary specificity in discrimination of molecular structures. Our understanding of immune phylogeny over the past decades has tried to reconcile immunity from a vertebrate standpoint. While informative, such approaches cannot completely address the complex nature of selective pressures brought to bear by the complex microbiota (including pathogens) that co-exist with all metazoans. In recent years, comparative studies (and new technologies) have broadened our concepts of immunity from a systems-wide perspective. Unexpected findings, e.g., genetic expansions of innate receptors, high levels of polymorphism, RNA-based forms of generating diversity, adaptive evolution and functional divergence of gene families and the recognition of novel mediators of adaptive immunity, prompt us to reconsider the very nature of immunity. Even fundamental paradigms as to how the jawed vertebrate adaptive immune system should be structured for “optimal” recognition potential have been disrupted more than once (e.g., the discovery of the multicluster organization and germline joining of immunoglobulin genes in sharks, gene conversion as a mechanism of somatic diversification, absence of IgM or MHC II in certain teleost fishes). Mechanistically, concepts of innate immune memory, often referred to as “trained memory,” have been realized further, with the development of new discoveries in studies of epigenetic regulation of somatic lineages. Immune systems innovate and adapt in a taxon-specific manner, driven by the complexity of interactions with microbial symbionts (commensals, mutualists and pathogens). Immune systems are shaped by selective forces that reflect consequences of dynamic interactions with microbial environments as well as a capacity for rapid change that can be facilitated by genomic instabilities. We have learned that characterizing receptors and receptor interactions is not necessarily the most significant component in understanding the evolution of immunity. Rather, such a subject needs to be understood from a more global perspective and will necessitate re-consideration of the physical barriers that afford protection and the developmental processes that create them. By far, the most significant paradigm shifts in our understanding of immunity and the infection process has been that microbes no longer are considered to be an automatic cause or consequence of illness, but rather integral components of normal physiology and homeostasis. Immune phylogeny has been shaped not only by an arms race with pathogens but also perhaps by mutualistic interactions with resident microbes. This Research Topic updates and extends the previous eBook on Changing Views of the Evolution of Immunity and contains peer-reviewed submissions of original research, reviews and opinions.

This report recommends improvements to two areas of patent law policies affecting how well a patent gives notice to the public of what technology is protected and remedies for patent infringement. The report provides valuable insights on how courts can reform the patent system to best serve consumers. It recognizes that patents play a critical role in encouraging innovation, but it also observes that some strategies by patent holders risk distorting competition and deterring innovation. This is especially true for activity driven by poor patent notice, and by remedies that do not align the compensation received by patent holders for infringement with the economic value of their patented inventions. This is a print on demand report.

Ever since the pioneering work of Darwin and Wallace, evolutionary biologists have attempted to understand the evolutionary dynamics of genetic systems. A range of theories on evolutionary ratesfrom static to gradual to punctuated to quantumhave been developed, primarily by comparing morphological changes over geological timescales as described in the fossil record. Recent studies, however, are beginning to change the way that we view evolutionary patterns and processes. New paleontological, experimental, molecular, and genomic investigations are providing a tremendous amount of novel data and fresh perspectives, offering valuable insights on the rates of evolutionary change, particularly in fast-evolving genetic systems. Rapidly Evolving Genes and Genetic Systems captures these recent exciting developments across a broad range of morphological, molecular, cellular, developmental, and genetic investigations in both natural and experimental populations over a diversity of life forms. The book provides a fascinating series of case studies that exemplify rapid evolution, and showcases the diversity of rapidly evolving genes and genetic systems, emphasizing the extremely important roles that they play in adaptation, speciation, and the generation and maintenance of a diversity of biological traits and properties. This exciting collection showcases the latest research of more than 50 eminent evolutionary biologists. It will be suitable for senior undergraduate students, graduate students, researchers, and for all those interested in the study of evolution.

This book offers a definitive resource that bridges biology and evolutionary computation. The authors have written an introduction to biology and bioinformatics for computer scientists, plus an introduction to evolutionary computation for biologists and for computer scientists unfamiliar with these techniques.

Selected papers and abstracts of the symposium held August 6 through 9, 2011, Billings, Montana

Human illnesses can be understood as damage to those adaptations that we took on at various stages in our evolution from pre-life molecules to modern Homo sapiens. Preventing these illnesses entails avoiding what causes the damage — which too frequently are the everyday hazards of twenty-first-century life, as the chart below shows: Level of Evolution / Cause of adaptive failure / resulting disease or problem Pre-life / Environmental poisons / Certain birth defects Single cell (bacteria and amoeba-like) / Viral infection / Colds/flu/HIV Morula (sponge-like) / Cellular stress / Cancer Chordate / Physical stress / Back pain Fish / Excess dietary salt / Hypertension/heart disease Amphibian / Tobacco smoke / Lung cancer/emphysema Lower primate / Excess dietary sugar / Diabetes mellitus Higher primate / Vitamin C deficiency / Scurvy Ape / Excess dietary protein / Gout Homo sapiens / Reduced dietary variety / Nutritionaldiseases/food allergies

Animal evolution has always been at the core of Biology, but even today many fundamental questions remain open. The field of animal ‘evo-devo’ is leveraging recent technical and conceptual advances in development, paleontology, genomics and transcriptomics to propose radically different answers to traditional evolutionary controversies. This book is divided into four parts, each of which approaches animal evolution from a different perspective. The first part (chapters 2 and 3) investigates how new sources of evidence have changed conventional views of animal origins, while the second (chapters 4–8) addresses the connection between embryogenesis and evolution, and the genesis of cellular, tissue and morphological diversity. The third part (chapters 9 and 10) investigates how big data in molecular biology is transforming our understanding of the mechanisms governing morphological change in animals. In closing, the fourth part (chapters 11–13) explores new theoretical and conceptual approaches to animal evolution. ‘Old questions and young approaches to animal evolution’ offers a comprehensive and updated view of animal evolutionary biology that will serve both as a first step into this fascinating field for students and university educators, and as a review of complementary approaches for researchers.