Reconstructing the Past
Reconstructing the Past

Author: Elliott Sober

Publisher: MIT Press

Published: 1991-02-05

Total Pages: 298

ISBN-13: 9780262691444

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Reconstructing the Past seeks to clarify and help resolve the vexing methodological issues that arise when biologists try to answer such questions as whether human beings are more closely related to chimps than they are to gorillas. It explores the case for considering the philosophical idea of simplicity/parsimony as a useful principle for evaluating taxonomic theories of evolutionary relationships. For the past two decades, evolutionists have been vigorously debating the appropriate methods that should be used in systematics, the field that aims at reconstructing phylogenetic relationships among species. This debate over phylogenetic inference, Elliott Sober observes, raises broader questions of hypothesis testing and theory evaluation that run head on into long standing issues concerning simplicity/parsimony in the philosophy of science. Sober treats the problem of phylogenetic inference as a detailed case study in which the philosophical idea of simplicity/parsimony can be tested as a principle of theory evaluation. Bringing together philosophy and biology, as well as statistics, Sober builds a general framework for understanding the circumstances in which parsimony makes sense as a tool of phylogenetic inference. Along the way he provides a detailed critique of parsimony in the biological literature, exploring the strengths and limitations of both statistical and nonstatistical cladistic arguments.

Reconstructing Evolution
Reconstructing Evolution

Author: Olivier Gascuel

Publisher: Oxford University Press

Published: 2007-06-28

Total Pages: 349

ISBN-13: 0199208220

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Evolution is a complex process, acting at multiple scales, from DNA sequences and proteins to populations of species. Understanding and reconstructing evolution is of major importance in numerous subfields of biology. For example, phylogenetics and sequence evolution is central to comparative genomics, attempts to decipher genomes, and molecular epidemiology. Phylogenetics is also the focal point of large-scale international biodiversity assessment initiatives such as the 'Tree ofLife' project, which aims to build the evolutionary tree for all extant species.Since the pioneering work in phylogenetics in the 1960s, models have become increasingly sophisticated to account for the inherent complexity of evolution. They rely heavily on mathematics and aim at modelling and analyzing biological phenomena such as horizontal gene transfer, heterogeneity of mutation, and speciation and extinction processes. This book presents these recent models, their biological relevance, their mathematical basis, their properties, and the algorithms to infer them fromdata. A number of subfields from mathematics and computer science are involved: combinatorics, graph theory, stringology, probabilistic and Markov models, information theory, statistical inference, Monte Carlo methods, continuous and discrete algorithmics.This book arises from the Mathematics of Evolution & Phylogenetics meeting at the Mathematical Institute Henri Poincaré, Paris, in June 2005 and is based on the outstanding state-of-the-art reports presented by the conference speakers. Ten chapters - based around five themes - provide a detailed overview of key topics, from the underlying concepts to the latest results, some of which are at the forefront of current research.

Ancestral Sequence Reconstruction
Ancestral Sequence Reconstruction

Author: David A Liberles

Publisher: Oxford University Press

Published: 2007-05-31

Total Pages: 267

ISBN-13: 0199299188

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Ancestral sequence reconstruction is a technique of growing importance in molecular evolutionary biology and comparative genomics. As a powerful tool for testing evolutionary and ecological hypotheses, as well as uncovering the link between sequence and molecular phenotype, there are potential applications in a range of fields.Ancestral Sequence Reconstruction starts with a historical overview of the field, before discussing the potential applications in drug discovery and the pharmaceutical industry. This is followed by a section on computational methodology, which provides a detailed discussion of the available methods for reconstructing ancestral sequences (including their advantages, disadvantages, and potential pitfalls). Purely computational applications of the technique are then covered, including wholeproteome reconstruction. Further chapters provide a detailed discussion on taking computationally reconstructed sequences and synthesizing them in the laboratory. The book concludes with a description of the scientific questions where experimental ancestral sequence reconstruction has been utilized toprovide insights and inform future research.This research level text provides a first synthesis of the theories, methodologies and applications associated with ancestral sequence recognition, while simultaneously addressing many of the hot topics in the field. It will be of interest and use to both graduate students and researchers in the fields of molecular biology, molecular evolution, and evolutionary bioinformatics.

Mathematics of Evolution and Phylogeny
Mathematics of Evolution and Phylogeny

Author: Olivier Gascuel

Publisher: OUP Oxford

Published: 2005-02-24

Total Pages: 444

ISBN-13: 9780191513732

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This book considers evolution at different scales: sequences, genes, gene families, organelles, genomes and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation. Recent years have witnessed rapid progress in the mathematics of evolution and phylogeny, with models and methods becoming more realistic, powerful, and complex. Aimed at graduates and researchers in phylogenetics, mathematicians, computer scientists and biologists, and including chapters by leading scientists: A. Bergeron, D. Bertrand, D. Bryant, R. Desper, O. Elemento, N. El-Mabrouk, N. Galtier, O. Gascuel, M. Hendy, S. Holmes, K. Huber, A. Meade, J. Mixtacki, B. Moret, E. Mossel, V. Moulton, M. Pagel, M.-A. Poursat, D. Sankoff, M. Steel, J. Stoye, J. Tang, L.-S. Wang, T. Warnow, Z. Yang, this book of contributed chapters explains the basis and covers the recent results in this highly topical area.

Tangled Trees
Tangled Trees

Author: Roderic D. M. Page

Publisher: University of Chicago Press

Published: 2003

Total Pages: 364

ISBN-13: 9780226644660

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In recent years, the use of molecular data to build phylogenetic trees and sophisticated computer-aided techniques to analyze them have led to a revolution in the study of cospeciation. Tangled Trees provides an up-to-date review and synthesis of current knowledge about phylogeny, cospeciation, and coevolution. The opening chapters present various methodological and theoretical approaches, ranging from the well-known parsimony approach to "jungles" and Bayesian statistical models. Then a series of empirical chapters discusses detailed studies of cospeciation involving vertebrate hosts and their parasites, including nematodes, viruses, and lice. Tangled Trees will be welcomed by researchers in a wide variety of fields, from parasitology and ecology to systematics and evolutionary biology. Contributors: Sarah Al-Tamimi, Michael A. Charleston, Dale H. Clayton, James W. Demastes, Russell D. Gray, Mark S. Hafner, John P. Huelsenbeck, J.-P. Hugot, Kevin P. Johnson, Peter Kabat, Bret Larget, Joanne Martin, Yannis Michalakis, Roderic D. M. Page, Ricardo L. Palma, Adrian M. Paterson, Susan L. Perkins, Andy Purvis, Bruce Rannala, David L. Reed, Fredrik Ronquist, Theresa A. Spradling, Jason Taylor, Michael Tristem

Reconstructing Earth
Reconstructing Earth

Author: Braden Allenby

Publisher: Island Press

Published: 2013-04-15

Total Pages: 220

ISBN-13: 1597266205

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The Earth's biological, chemical, and physical systems are increasingly shaped by the activities of one species-ours. In our decisions about everything from manufacturing technologies to restaurant menus, the health of the planet has become a product of human choice. Environmentalism, however, has largely failed to adapt to this new reality. Reconstructing Earth offers seven essays that explore ways of developing a new, more sophisticated approach to the environment that replaces the fantasy of recovering pristine landscapes with a more grounded viewpoint that can foster a better relationship between humans and the planet. Braden Allenby, a lawyer with degrees in both engineering and environmental studies, explains the importance of technological choice, and how that factor is far more significant in shaping our environment (in ways both desirable and not) than environmental controls. Drawing on his varied background and experience in both academia and the corporate world, he describes the emerging field of "earth systems engineering and management," which offers an integrated approach to understanding and managing complex human/natural systems that can serve as a basis for crafting better, more lasting solutions to widespread environmental problems. Reconstructing Earth not only critiques dysfunctional elements of current environmentalism but establishes a foundation for future environmental management and progress, one built on an understanding of technological evolution and the cultural systems that support modern technologies. Taken together, the essays offer an important means of developing an environmentalism that is robust and realistic enough to address the urgent realities of our planet. Reconstructing Earth is a thought-provoking new work for anyone concerned with the past or future of environmental thought, including students and teachers of environmental studies, environmental policy, technology policy, technological evolution, or sustainability.

Reconstructing Human Origins
Reconstructing Human Origins

Author: Glenn C. Conroy

Publisher: W. W. Norton & Company

Published: 2012-02-13

Total Pages: 8

ISBN-13: 0393912892

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Reconstructing Human Origins is the most authoritative, comprehensive, and popular paleoanthropology textbook available. Respected anthropologists Glenn Conroy and new coauthor Herman Pontzer use clear writing and abundant, carefully chosen illustrations to illuminate key concepts and help students get the most out of the course. This definitive paleoanthropology text has been fully revised to keep pace with all of the exciting recent developments in the field.

Life's Splendid Drama
Life's Splendid Drama

Author: Peter J. Bowler

Publisher: University of Chicago Press

Published: 1996-11-15

Total Pages: 556

ISBN-13: 9780226069210

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As Bowler tracks major scientific debates over the emergence of the vertebrates, the origins of the main types of living animals, and the rise and extinction of groups such as the dinosaurs, his richly detailed accounts bring to light complex interactions among specialists in various fields of biology.

Reconstructing the Tree of Life
Reconstructing the Tree of Life

Author: Trevor R. Hodkinson

Publisher: CRC Press

Published: 2006-12-26

Total Pages: 374

ISBN-13: 1420009532

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To document the world's diversity of species and reconstruct the tree of life we need to undertake some simple but mountainous tasks. Most importantly, we need to tackle species rich groups. We need to collect, name, and classify them, and then position them on the tree of life. We need to do this systematically across all groups of organisms and b

Molecular Evolution
Molecular Evolution

Author: Roderick D.M. Page

Publisher: John Wiley & Sons

Published: 2009-07-14

Total Pages: 352

ISBN-13: 1444313363

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The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.