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Author: Olivier Gascuel
Publisher: Oxford University Press
ISBN: 0199208220
Category : Mathematics
Languages : en
Pages : 349
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Book Description
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.
Author: Elliott Sober
Publisher: MIT Press
ISBN: 9780262691444
Category : Psychology
Languages : en
Pages : 298
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Book Description
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.
Author: Olivier Gascuel
Publisher: Oxford University Press
ISBN: 0199208220
Category : Mathematics
Languages : en
Pages : 349
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Book Description
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.
Author: David A Liberles
Publisher: Oxford University Press
ISBN: 0199299188
Category : Science
Languages : en
Pages : 267
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Book Description
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.
Author: Olivier Gascuel
Publisher: OUP Oxford
ISBN: 9780191513732
Category : Mathematics
Languages : en
Pages : 444
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Book Description
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.
Author: Roderic D. M. Page
Publisher: University of Chicago Press
ISBN: 9780226644660
Category : Biography & Autobiography
Languages : en
Pages : 364
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Book Description
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
Author: Braden Allenby
Publisher: Island Press
ISBN: 1597266205
Category : Science
Languages : en
Pages : 220
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Book Description
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.
Author: Trevor R. Hodkinson
Publisher: CRC Press
ISBN: 1420009532
Category : Mathematics
Languages : en
Pages : 374
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Book Description
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
Author: National Academy of Sciences
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 388
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Book Description
The Arthur M. Sackler Colloquia of the National Academy of Sciences address scientific topics of broad and current interest, cutting across the boundaries of traditional disciplines. Each year, four or five such colloquia are scheduled, typically two days in length and international in scope. Colloquia are organized by a member of the Academy, often with the assistance of an organizing committee, and feature presentations by leading scientists in the field and discussions with a hundred or more researchers with an interest in the topic. Colloquia presentations are recorded and posted on the National Academy of Sciences Sackler colloquia website and published on CD-ROM. These Colloquia are made possible by a generous gift from Mrs. Jill Sackler, in memory of her husband, Arthur M. Sackler.
Author: Glenn C. Conroy
Publisher: W. W. Norton & Company
ISBN: 0393912892
Category : Social Science
Languages : en
Pages : 8
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Book Description
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.
Author: Murray Clarke
Publisher: MIT Press
ISBN: 9780262262194
Category : Philosophy
Languages : en
Pages : 200
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Book Description
A study of the philosophical implications of evolutionary psychology, suggesting that knowledge is a set of natural kinds housed in the modules of a massively modular mind. In Reconstructing Reason and Representation, Murray Clarke offers a detailed study of the philosophical implications of evolutionary psychology. In doing so, he offers new solutions to key problems in epistemology and philosophy of mind, including misrepresentation and rationality. He proposes a naturalistic approach to reason and representation that is informed by evolutionary psychology, and, expanding on the massive modularity thesis advanced in work by Leda Cosmides and John Tooby, argues for a modular, adapticist account of misrepresentation and knowledge. Just as the reliability of representation can be defended on the basis of an account of the proper function of cognitive modularity, misrepresentation can be explained through an appeal to the "gap theory," by noting the divergence between the proper and actual domains of cognitive modules in a massively modular mind. Clarke argues for an externalist, modular reliabilism by suggesting that evolution has equipped us with generally reliable inferential systems even if they do not always produce true beliefs. He argues that reliable deductive and inductive inference occurs only when cognitive modules deal with actual domains that are sufficiently similar to their proper domains. This psychologically informed, naturalized adapticism leads to the suggestion that knowledge is a set of natural kinds housed in the modules of a massively modular mind. Typically, the proper function of these cognitive modules is to provide us with truths that enable us to satisfy our basic biological needs. Beyond reasoning modules, other cognitive modules discussed include the ability to orient ourselves in space, and our abilities with language, numbers, object reasoning, and social understanding. Clarke also defends Cosmides and Tooby's massive modularity hypothesis against such critics as Jerry Fodor by demonstrating that these critics consistently misrepresent Cosmides and Tooby's position.
