Phylogenetics

Author : E. O. Wiley,Bruce S. Lieberman
Publisher : John Wiley & Sons
Page : 444 pages
File Size : 48,9 Mb
Release : 2011-06-07
Category : Science
ISBN : 9780470905968

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Phylogenetics by E. O. Wiley,Bruce S. Lieberman Pdf

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.

Author : Charles Semple,Mike Steel,Both in the Department of Mathematics and Statistics Mike Steel
Publisher : Oxford University Press on Demand
Page : 258 pages
File Size : 55,8 Mb
Release : 2003
Category : Computers
ISBN : 0198509421

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Phylogenetics by Charles Semple,Mike Steel,Both in the Department of Mathematics and Statistics Mike Steel Pdf

'Phylogenetics' is the reconstruction and analysis of phylogenetic (evolutionary) trees and networks based on inherited characteristics. It is a flourishing area of intereaction between mathematics, statistics, computer science and biology.The main role of phylogenetic techniques lies in evolutionary biology, where it is used to infer historical relationships between species. However, the methods are also relevant to a diverse range of fields including epidemiology, ecology, medicine, as well as linguistics and cognitive psychologyThis graduate-level book, based on the authors lectures at The University of Canterbury, New Zealand, focuses on the mathematical aspects of phylogenetics. It brings together the central results of the field (providing proofs of the main theorem), outlines their biological significance,and indicateshow algorithms may be derived. The presentation is self-contained and relies on discrete mathematics with some probability theory. A set of exercises and at least one specialist topic ends each chapter.This book is intended for biologists interested in the mathematical theory behind phylogenetic methods, and for mathematicians, statisticians, and computer scientists eager to learn about this emerging area of discrete mathematics.'Phylogenetics' in the 24th volume in the Oxford Lecture Series in Mathematics and its Applications. This series contains short books suitable for graduate students and researchers who want a well-written account of mathematics that is fundamental to current to research. The series emphasises futuredirections of research and focuses on genuine applications of mathematics to finance, engineering and the physical and biological sciences.

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 221 pages
File Size : 41,7 Mb
Release : 2006-11-25
Category : Science
ISBN : 9780387351001

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Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis Pdf

This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.

Author : Ming-Hui Chen,Lynn Kuo,Paul O. Lewis
Publisher : CRC Press
Page : 398 pages
File Size : 50,8 Mb
Release : 2014-05-27
Category : Mathematics
ISBN : 9781466500792

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Bayesian Phylogenetics by Ming-Hui Chen,Lynn Kuo,Paul O. Lewis Pdf

Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.

Author : Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey
Publisher : Cambridge University Press
Page : 750 pages
File Size : 43,5 Mb
Release : 2009-03-26
Category : Science
ISBN : 9780521877107

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The Phylogenetic Handbook by Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey Pdf

A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Author : Xuhua Xia
Publisher : CRC Press
Page : 366 pages
File Size : 54,5 Mb
Release : 2020-04-13
Category : Science
ISBN : 9780429759314

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A Mathematical Primer of Molecular Phylogenetics by Xuhua Xia Pdf

This volume, A Mathematical Primer of Molecular Phylogenetics, offers a unique perspective on a number of phylogenetic issues that have not been covered in detail in previous publications. The volume provides sufficient mathematical background for young mathematicians and computational scientists, as well as mathematically inclined biology students, to make a smooth entry into the expanding field of molecular phylogenetics. The book will also provide sufficient details for researchers in phylogenetics to understand the workings of existing software packages used. The volume offers comprehensive but detailed numerical illustrations to render difficult mathematical and computational concepts in molecular phylogenetics accessible to a variety of readers with different academic background. The text includes examples of solved problems after each chapter, which will be particularly helpful for fourth-year undergraduates, postgraduates, and postdoctoral students in biology, mathematics and computer sciences. Researchers in molecular biology and evolution will find it very informative as well.

Author : Masatoshi Nei,Sudhir Kumar
Publisher : Oxford University Press
Page : 352 pages
File Size : 52,7 Mb
Release : 2000-07-27
Category : Science
ISBN : 9780199881222

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Molecular Evolution and Phylogenetics by Masatoshi Nei,Sudhir Kumar Pdf

During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.

Author : Ibrokhim Y. Abdurakhmonov
Publisher : BoD – Books on Demand
Page : 122 pages
File Size : 40,6 Mb
Release : 2017-09-06
Category : Medical
ISBN : 9789535134992

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Phylogenetics by Ibrokhim Y. Abdurakhmonov Pdf

Phylogenetics aims to study the evolutionary relatedness of living organisms in our planet. Its application is extended to the key areas such as evolution, classification and taxonomy of living organisms; ecology, diversity, and conservation biology of agrobiocenosis; monitoring of pathogen spread, outbreaks and source of transmissions, forensic analyses, etc. Historically, phylogenetics studies were prevalently based on morphological features of species that helped to classify the 'Tree of Life' on Earth. Modern phylogenetics studies, however, rely more heavily on DNA sequences. In this Phylogenetics book, we aimed to present readers the latest developments in phylogenetics studies that highlight multi-kingdom systems, reticulated evolution and conservation biology of living organisms as well as 'omics'-based phylogenetics advances.

Author : Tandy Warnow
Publisher : Cambridge University Press
Page : 399 pages
File Size : 52,5 Mb
Release : 2017-11-02
Category : Computers
ISBN : 9781107184718

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Computational Phylogenetics by Tandy Warnow Pdf

This book presents the foundations of phylogeny estimation and technical material enabling researchers to develop improved computational methods.

Author : Tandy Warnow
Publisher : Springer
Page : 410 pages
File Size : 45,8 Mb
Release : 2019-04-08
Category : Computers
ISBN : 9783030108373

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Bioinformatics and Phylogenetics by Tandy Warnow Pdf

This 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 : David A. Baum,Stacey D. Smith
Publisher : Roberts
Page : 0 pages
File Size : 50,8 Mb
Release : 2012-08-10
Category : Science
ISBN : 1936221160

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Tree Thinking: An Introduction to Phylogenetic Biology by David A. Baum,Stacey D. Smith Pdf

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.

Author : Roderick D.M. Page,Edward C. Holmes
Publisher : John Wiley & Sons
Page : 352 pages
File Size : 45,7 Mb
Release : 2009-07-14
Category : Science
ISBN : 9781444313369

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Molecular Evolution by Roderick D.M. Page,Edward C. Holmes Pdf

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.

Author : E. O. Wiley,Bruce S. Lieberman
Publisher : John Wiley & Sons
Page : 444 pages
File Size : 45,8 Mb
Release : 2011-10-11
Category : Science
ISBN : 9781118017876

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Phylogenetics by E. O. Wiley,Bruce S. Lieberman Pdf

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.

Author : Larissa Mendoza Straffon
Publisher : Springer
Page : 202 pages
File Size : 53,5 Mb
Release : 2016-02-10
Category : Science
ISBN : 9783319259284

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Cultural Phylogenetics by Larissa Mendoza Straffon Pdf

This book explores the potential and challenges of implementing evolutionary phylogenetic methods in archaeological research, by discussing key concepts and presenting concrete applications of these approaches. The volume is divided into two parts: The first covers the theoretical and conceptual implications of using evolution-based models in the sociocultural domain, illustrates the sorts of questions that these methods can help answer, and invites the reader to reflect on the opportunities and limitations of these perspectives. The second part comprises case studies that address relevant empirical issues, such as inferring patterns and rates of cultural transmission, detecting selective pressures in cultural evolution, and explaining the nature of cultural variation. This book will appeal to archaeologists interested in applying evolutionary thinking and inferential methods to their field, and to anyone interested in cultural evolution studies.

Author : Juan Wang,Quan Zou,Qiguo Dai
Publisher : Frontiers Media SA
Page : 107 pages
File Size : 52,8 Mb
Release : 2022-08-03
Category : Science
ISBN : 9782889763443

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Methods and Applications in Molecular Phylogenetics by Juan Wang,Quan Zou,Qiguo Dai Pdf