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“Biodiversity” refers to the variety of life. It is now agreed that there is a “biodiversity crisis”, corresponding to extinction rates of species that may be 1000 times what is thought to be “normal”. Biodiversity science has a higher profile than ever, with the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services involving more than 120 countries and 1000s of scientists. At the same time, the discipline is re-evaluating its foundations – including its philosophy and even core definitions. The value of biodiversity is being debated. In this context, the tree of life (“phylogeny”) is emerging as an important way to look at biodiversity, with relevance cutting across current areas of concern – from the question of resilience within ecosystems, to conservation priorities for globally threatened species – while capturing the values of biodiversity that have been hard to quantify, including resilience and maintaining options for future generations. This increased appreciation of the importance of conserving “phylogenetic diversity”, from microbial communities in the human gut to global threatened species, has inevitably resulted in an explosion of new indices, methods, and case studies. This book recognizes and responds to the timely opportunity for synthesis and sharing experiences in practical applications. The book recognizes that the challenge of finding a synthesis, and building shared concepts and a shared toolbox, requires both an appreciation of the past and a look into the future. Thus, the book is organized as a flow from history, concepts and philosophy, through to methods and tools, and followed by selected case studies. A positive vision and plan of action emerges from these chapters, that includes coping with inevitable uncertainties, effectively communicating the importance of this “evolutionary heritage” to the public and to policy-makers, and ultimately contributing to biodiversity conservation policy from local to global scales.
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.
This book is about phylogenetic diversity as an approach to reduce biodiversity losses in this period of mass extinction. Chapters in the first section deal with questions such as the way we value phylogenetic diversity among other criteria for biodiversity conservation; the choice of measures; the loss of phylogenetic diversity with extinction; the importance of organisms that are deeply branched in the tree of life, and the role of relict species. The second section is composed by contributions exploring methodological aspects, such as how to deal with abundance, sampling effort, or conflicting trees in analysis of phylogenetic diversity. The last section is devoted to applications, showing how phylogenetic diversity can be integrated in systematic conservation planning, in EDGE and HEDGE evaluations. This wide coverage makes the book a reference for academics, policy makers and stakeholders dealing with biodiversity conservation.
Understanding the history and philosophy of biological systematics (phylogenetics, taxonomy and classification of living things) is key to successful practice of the discipline. In this thoroughly revised Third Edition of the classic Biological Systematics, Andrew V. Z. Brower and Randall T. Schuh provide an updated account of cladistic principles and techniques, emphasizing their empirical and epistemological clarity. Brower and Schuh cover: -the history and philosophy of systematics -the mechanics and methods of character analysis, phylogenetic inference, and evaluation of results -the practical application of systematic results to: -biological classification -adaptation and coevolution -biodiversity, and conservation -new chapters on species and molecular clocks Biological Systematics is both a textbook for students studying systematic biology and a desk reference for practicing systematists. Part explication of concepts and methods, part exploration of the underlying epistemology of systematics, This third edition addresses why some methods are more empirically sound than others.
The statistical analysis of discrete multivariate data has received a great deal of attention in the statistics literature over the past two decades. The develop ment ofappropriate models is the common theme of books such as Cox (1970), Haberman (1974, 1978, 1979), Bishop et al. (1975), Gokhale and Kullback (1978), Upton (1978), Fienberg (1980), Plackett (1981), Agresti (1984), Goodman (1984), and Freeman (1987). The objective of our book differs from those listed above. Rather than concentrating on model building, our intention is to describe and assess the goodness-of-fit statistics used in the model verification part of the inference process. Those books that emphasize model development tend to assume that the model can be tested with one of the traditional goodness-of-fit tests 2 2 (e.g., Pearson's X or the loglikelihood ratio G ) using a chi-squared critical value. However, it is well known that this can give a poor approximation in many circumstances. This book provides the reader with a unified analysis of the traditional goodness-of-fit tests, describing their behavior and relative merits as well as introducing some new test statistics. The power-divergence family of statistics (Cressie and Read, 1984) is used to link the traditional test statistics through a single real-valued parameter, and provides a way to consolidate and extend the current fragmented literature. As a by-product of our analysis, a new 2 2 statistic emerges "between" Pearson's X and the loglikelihood ratio G that has some valuable properties.
This volume reviews the historical roots and theoretical foundations of biological systematics in an approachable text. The author outlines the structure and main tasks of systematics. Conceptual history is characterized as a succession of scientific revolutions. The philosophical foundations of systematic research are briefly reviewed as well as the structure and content of taxonomic theories. Most important research programs in systematics are outlined. The book includes analysis of the principal problematic issues as "scientific puzzles" in systematics. This volume is intended for professional taxonomists, biologists of various specialties, students, as well as all those interested in the history and theory of biology and natural sciences. Key Features Considers the conceptual history of systematics as the framework of evolutionary epistemology Builds a hierarchically organized quasi-axiomatic system of taxonomic theory Contends that more reductionist taxonomic concepts are less objective Supports taxonomic pluralism by non-classic philosophy of science as a normal condition of systematics Documents that "taxonomic puzzles" result from conflict between monistic and pluralistic attitudes Related Titles de Queiroz, K. et al., eds. Phylonyms: A Companion to the PhyloCode (ISBN 978-1-1383-3293-5) Sigwart, J. D. What Species Mean: A User's Guide to the Units of Biodiversity (ISBN 978-1-4987-9937-9) Rieppel, O. Phylogenetic Systematics: Haeckel to Hennig (ISBN 978-1-4987-5488-0) Wilkins, J. S. Species: The Evolution of the Idea, 2nd ed. (ISBN 978-1-1380-5574-2)
Phylogenetic Systematics: Haeckel to Hennig traces the development of phylogenetic systematics against the foil of idealistic morphology through 100 years of German biology. It starts with the iconic Ernst Haeckel-the German Darwin from Jena-and the evolutionary morphology he developed. It ends with Willi Hennig, the founder of modern phylogenetic
Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or “phylogenies.” However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives. Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set of problems, valuable for both students and teachers. Tree Thinking is must-have textbook for any student seeking a solid foundation in this fundamental area of evolutionary biology.
This book documents Willi Hennig's founding of phylogenetic systematics and the relevancy of his work for the future of cladistics.