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Author: Marco Salemi
Publisher: Cambridge University Press
Published: 2009-03-26
Total Pages: 750
ISBN-13: 0521877105
DOWNLOAD EBOOKA broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.
Author: Mike Steel
Publisher: SIAM
Published: 2016-09-29
Total Pages: 302
ISBN-13: 161197447X
DOWNLOAD EBOOKPhylogenetics is a topical and growing area of research. Phylogenies (phylogenetic trees and networks) allow biologists to study and graph evolutionary relationships between different species. These are also used to investigate other evolutionary processes?for example, how languages developed or how different strains of a virus (such as HIV or influenza) are related to each other. This self-contained book addresses the underlying mathematical theory behind the reconstruction and analysis of phylogenies. The theory is grounded in classical concepts from discrete mathematics and probability theory as well as techniques from other branches of mathematics (algebra, topology, differential equations). The biological relevance of the results is highlighted throughout. The author supplies proofs of key classical theorems and includes results not covered in existing books, emphasizes relevant mathematical results derived over the past 20 years, and provides numerous exercises, examples, and figures.
Author: Joseph Felsenstein
Publisher: Sinauer Associates Incorporated
Published: 2004-01
Total Pages: 664
ISBN-13: 9780878931774
DOWNLOAD EBOOKPhylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.
Author: Olivier Gascuel
Publisher: OUP Oxford
Published: 2005-02-24
Total Pages: 444
ISBN-13: 9780191513732
DOWNLOAD EBOOKThis 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: Tandy Warnow
Publisher: Springer
Published: 2019-04-08
Total Pages: 426
ISBN-13: 3030108376
DOWNLOAD EBOOKThis volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Author: Rolf G. Beutel
Publisher: Walter de Gruyter
Published: 2013-12-12
Total Pages: 532
ISBN-13: 3110264048
DOWNLOAD EBOOKIn the last decades a remarkable renaissance has materialized in insect morphology, mainly triggered by the development of new cutting-edge technologies. This is an exciting time for biological synthesis where the mysteries and data derived from genomes can be combined with centuries of data from morphology and development. And, now, more than ever, detailed knowledge of morphology is essential to understanding the evolution of all groups of organisms. In this “age of phylogenomics” researchers rely on morphological data to support molecular findings, test complex evolutionary scenarios, and for placing fossil taxa. This textbook provides an in-depth treatment of the structures and the phylogeny of the megadiverse Hexapoda. The first part presents an up-to-date overview of general insect morphology with detailed drawings, scanning electron micrographs, and 3-D reconstructions. Also included is a chapter covering innovative morphological techniques (e.g., μ-computer tomography, 3-D modeling), brief treatments of insect development and phylogenetic methods, and a comprehensive morphological glossary. The second part is of a modern synthesis of insect systematics that includes taxon-specific morphological information for all Orders. The work is an invaluable reference for students and researchers working in all facets of biology and is a must for evolutionary biologists. A detailed understanding of morphology is essential in unraveling phylogenetic relationships and developing complex evolutionary scenarios. Increasingly researchers in phylogenomics are re/turning to morphological data to support their findings, while the development of new cutting-edge technologies has further increased interest in this growing field. This definitive handbook provides an in-depth treatment of insect morphology. The first part presents an up-to-date overview of insect morphology with detailed drawings, brilliant scanning electron micrographs and 3-D reconstructions as interactive PDFs. This is complemented by a chapter on innovative morphological techniques (e.g., μ-computer tomography, 3-D modeling) and a comprehensive morphological glossary. The second part treats the state of the art in insect systematics and includes taxon-specific morphological information for all orders. Systematics are treated formally, with for example the arguments for relationships (“apomorphies”) always listed explicitly. The work is a useful reference for students and researchers working in different fields of biology and a must for those dealing with insects from an evolutionary perspective.
Author: László Zsolt Garamszegi
Publisher: Springer
Published: 2014-07-29
Total Pages: 553
ISBN-13: 3662435500
DOWNLOAD EBOOKPhylogenetic comparative approaches are powerful analytical tools for making evolutionary inferences from interspecific data and phylogenies. The phylogenetic toolkit available to evolutionary biologists is currently growing at an incredible speed, but most methodological papers are published in the specialized statistical literature and many are incomprehensible for the user community. This textbook provides an overview of several newly developed phylogenetic comparative methods that allow to investigate a broad array of questions on how phenotypic characters evolve along the branches of phylogeny and how such mechanisms shape complex animal communities and interspecific interactions. The individual chapters were written by the leading experts in the field and using a language that is accessible for practicing evolutionary biologists. The authors carefully explain the philosophy behind different methodologies and provide pointers – mostly using a dynamically developing online interface – on how these methods can be implemented in practice. These “conceptual” and “practical” materials are essential for expanding the qualification of both students and scientists, but also offer a valuable resource for educators. Another value of the book are the accompanying online resources (available at: http://www.mpcm-evolution.com), where the authors post and permanently update practical materials to help embed methods into practice.
Author: David A. Baum
Publisher: Roberts
Published: 2012-08-10
Total Pages: 0
ISBN-13: 9781936221165
DOWNLOAD EBOOKBaum 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.
Author: David R. Begun
Publisher: Springer Science & Business Media
Published: 2013-11-21
Total Pages: 430
ISBN-13: 1489900756
DOWNLOAD EBOOKAn insightful new work, Function, Phylogeny, and Fossils integrates two practices in paleobiology which are often separated - functional and phylogenetic analysis. The book summarizes the evidence on paleoenvironments at the most important Miocene hominoid sites and relates it to the pertinent fossil record. The contributors present the most up-to-date statements on the functional anatomy and likely behavior of the best known hominoids of this crucial period of ape and human evolution. A key feature is a comprehensive table listing 240 characteristics among 13 genera of living and extinct hominoids.
Author: E. O. Wiley
Publisher: John Wiley & Sons
Published: 2011-10-11
Total Pages: 444
ISBN-13: 1118017870
DOWNLOAD EBOOKThe 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.
