Inferring Phylogenies

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Inferring Phylogenies

Author : Joseph Felsenstein
Publisher : Sinauer Associates Incorporated
ISBN 13 : 9780878931774
Total Pages : 664 pages
Book Rating : 4.9/5 (317 download)

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Book Synopsis Inferring Phylogenies by : Joseph Felsenstein

Download or read book Inferring Phylogenies written by Joseph Felsenstein and published by Sinauer Associates Incorporated. This book was released on 2004-01 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenies, 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.

Inferring Phylogenies EBook

Author : Joseph Felsenstein
Publisher :
ISBN 13 : 9781605355009
Total Pages : 580 pages
Book Rating : 4.3/5 (55 download)

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Book Synopsis Inferring Phylogenies EBook by : Joseph Felsenstein

Download or read book Inferring Phylogenies EBook written by Joseph Felsenstein and published by . This book was released on 2003 with total page 580 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Phylogenetic Inference, Selection Theory, and History of Science

Author : Anthony William Fairbank Edwards
Publisher : Cambridge University Press
ISBN 13 : 1107111722
Total Pages : 553 pages
Book Rating : 4.1/5 (71 download)

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Book Synopsis Phylogenetic Inference, Selection Theory, and History of Science by : Anthony William Fairbank Edwards

Download or read book Phylogenetic Inference, Selection Theory, and History of Science written by Anthony William Fairbank Edwards and published by Cambridge University Press. This book was released on 2018-07-19 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: Seminal papers by A. W. F. Edwards, published together for the first time with commentaries from leading experts to contextualise his contribution.

Analysis of Phylogenetics and Evolution with R

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
ISBN 13 : 0387351000
Total Pages : 221 pages
Book Rating : 4.3/5 (873 download)

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Book Synopsis Analysis of Phylogenetics and Evolution with R by : Emmanuel Paradis

Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Tree Thinking: An Introduction to Phylogenetic Biology

Author : David A. Baum
Publisher : Roberts
ISBN 13 : 9781936221165
Total Pages : 0 pages
Book Rating : 4.2/5 (211 download)

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Book Synopsis Tree Thinking: An Introduction to Phylogenetic Biology by : David A. Baum

Download or read book Tree Thinking: An Introduction to Phylogenetic Biology written by David A. Baum and published by Roberts. This book was released on 2012-08-10 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Phylogenies and the Comparative Method in Animal Behavior

Author : Emília P. Martins
Publisher : Oxford University Press, USA
ISBN 13 : 0195092104
Total Pages : 429 pages
Book Rating : 4.1/5 (95 download)

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Book Synopsis Phylogenies and the Comparative Method in Animal Behavior by : Emília P. Martins

Download or read book Phylogenies and the Comparative Method in Animal Behavior written by Emília P. Martins and published by Oxford University Press, USA. This book was released on 1996 with total page 429 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the last ten years, the "comparative method" has been revolutionized by modern statistical ways of incorporating phylogenies into the design and analysis of comparative studies. The results of this revolution are particularly important in the study of animal behavior, which has relied on interspecific comparisons to infer universal trends and evolutionary patterns. The chapters of this edited volume consider the impact of modern phylogenetic comparative methods on the study of animal behavior and discuss the main issues that need to be considered in design and analysis of a comparative study, considers possible differences between the evolution of behavior and the evolution of morphology, and reviews how phylogenetic comparative studies have been used in certain areas of behavioral research.

Phylogenetic Inference, Selection Theory, and History of Science

Author : Rasmus Grønfeldt Winther
Publisher : Cambridge University Press
ISBN 13 : 1108613985
Total Pages : 553 pages
Book Rating : 4.1/5 (86 download)

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Book Synopsis Phylogenetic Inference, Selection Theory, and History of Science by : Rasmus Grønfeldt Winther

Download or read book Phylogenetic Inference, Selection Theory, and History of Science written by Rasmus Grønfeldt Winther and published by Cambridge University Press. This book was released on 2018-07-19 with total page 553 pages. Available in PDF, EPUB and Kindle. Book excerpt: A. W. F. Edwards is one of the most influential mathematical geneticists in the history of the discipline. One of the last students of R. A. Fisher, Edwards pioneered the statistical analysis of phylogeny in collaboration with L. L. Cavalli-Sforza, and helped establish Fisher's concept of likelihood as a standard of statistical and scientific inference. In this book, edited by philosopher of science Rasmus Grønfeldt Winther, Edwards's key papers are assembled alongside commentaries by leading scientists, discussing Edwards's influence on their own research and on thinking in their field overall. In an extensive interview with Winther, Edwards offers his thoughts on his contributions, their legacy, and the context in which they emerged. This book is a resource both for anyone interested in the history and philosophy of genetics, statistics, and science, and for scientists seeking to develop new algorithmic and statistical methods for understanding the genetic relationships between and among species both extant and extinct.

Phylogenies in Ecology

Author : Marc W. Cadotte
Publisher : Princeton University Press
ISBN 13 : 0691157685
Total Pages : 264 pages
Book Rating : 4.6/5 (911 download)

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Book Synopsis Phylogenies in Ecology by : Marc W. Cadotte

Download or read book Phylogenies in Ecology written by Marc W. Cadotte and published by Princeton University Press. This book was released on 2016-08-09 with total page 264 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenies in Ecology is the first book to critically review the application of phylogenetic methods in ecology, and it serves as a primer to working ecologists and students of ecology wishing to understand these methods. This book demonstrates how phylogenetic information is transforming ecology by offering fresh ways to estimate the similarities and differences among species, and by providing deeper, evolutionary-based insights on species distributions, coexistence, and niche partitioning. Marc Cadotte and Jonathan Davies examine this emerging area's explosive growth, allowing for this new body of hypotheses testing. Cadotte and Davies systematically look at all the main areas of current ecophylogenetic methodology, testing, and inference. Each chapter of their book covers a unique topic, emphasizes key assumptions, and introduces the appropriate statistical methods and null models required for testing phylogenetically informed hypotheses. The applications presented throughout are supported and connected by examples relying on real-world data that have been analyzed using the open-source programming language, R. Showing how phylogenetic methods are shedding light on fundamental ecological questions related to species coexistence, conservation, and global change, Phylogenies in Ecology will interest anyone who thinks that evolution might be important in their data.

Bioinformatics and Phylogenetics

Author : Tandy Warnow
Publisher : Springer
ISBN 13 : 3030108376
Total Pages : 410 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis Bioinformatics and Phylogenetics by : Tandy Warnow

Download or read book Bioinformatics and Phylogenetics written by Tandy Warnow and published by Springer. This book was released on 2019-04-08 with total page 410 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Molecular Evolution

Author : Roderick D.M. Page
Publisher : John Wiley & Sons
ISBN 13 : 1444313363
Total Pages : 352 pages
Book Rating : 4.4/5 (443 download)

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Book Synopsis Molecular Evolution by : Roderick D.M. Page

Download or read book Molecular Evolution written by Roderick D.M. Page and published by John Wiley & Sons. This book was released on 2009-07-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Phylogenetic Supertrees

Author : Olaf R.P. Bininda-Emonds
Publisher : Springer Science & Business Media
ISBN 13 : 1402023308
Total Pages : 547 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Phylogenetic Supertrees by : Olaf R.P. Bininda-Emonds

Download or read book Phylogenetic Supertrees written by Olaf R.P. Bininda-Emonds and published by Springer Science & Business Media. This book was released on 2004-05-31 with total page 547 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first book on "phylogenetic supertrees", a recent, but controversial development for inferring evolutionary trees. Rather than analyze the combined primary character data directly, supertree construction proceeds by combining the tree topologies derived from those data. This difference in strategy has allowed for the exciting possibility of larger, more complete phylogenies than are otherwise currently possible, with the potential to revolutionize evolutionarily-based research. This book provides a comprehensive look at supertrees, ranging from the methods used to build supertrees to the significance of supertrees to bioinformatic and biological research. Reviews of many the major supertree methods are provided and four new techniques, including a Bayesian implementation of supertrees, are described for the first time. The far-reaching impact of supertrees on biological research is highlighted both in general terms and through specific examples from diverse clades such as flowering plants, even-toed ungulates, and primates. The book also critically examines the many outstanding challenges and problem areas for this relatively new field, showing the way for supertree construction in the age of genomics. Interdisciplinary contributions from the majority of the leading authorities on supertree construction in all areas of the bioinformatic community (biology, computer sciences, and mathematics) will ensure that this book is a valuable reference with wide appeal to anyone interested in phylogenetic inference.

Biological Evolution and Statistical Physics

Author : M. Lässig
Publisher : Springer
ISBN 13 : 3540456929
Total Pages : 340 pages
Book Rating : 4.5/5 (44 download)

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Book Synopsis Biological Evolution and Statistical Physics by : M. Lässig

Download or read book Biological Evolution and Statistical Physics written by M. Lässig and published by Springer. This book was released on 2008-01-11 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: This set of lecture notes gives a first coherent account of a novel aspect of the living world that can be called biological information. The book presents both a pedagogical and state-of-the art roadmap of this rapidly evolving area and covers the whole field, from information which is encoded in the molecular genetic code to the description of large-scale evolution of complex species networks. The book will prove useful for all those who work at the interface of biology, physics and information science.

Computational Molecular Evolution

Author : Ziheng Yang
Publisher : Oxford University Press, USA
ISBN 13 : 0198566999
Total Pages : 374 pages
Book Rating : 4.1/5 (985 download)

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Book Synopsis Computational Molecular Evolution by : Ziheng Yang

Download or read book Computational Molecular Evolution written by Ziheng Yang and published by Oxford University Press, USA. This book was released on 2006-10-05 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.

Inferring Large Phylogenies

Author : Rutger Aldo Vos
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (112 download)

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Book Synopsis Inferring Large Phylogenies by : Rutger Aldo Vos

Download or read book Inferring Large Phylogenies written by Rutger Aldo Vos and published by . This book was released on 2006 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Phylogenetic trees are graph-like structures whose topology describes the inferred pattern of relationships among a set of biological entities, such as species or DNA sequences. Inference of these phylogenies typically involves evaluating large numbers of possible solutions and choosing the optimal topology, or set of topologies, from among all evaluated solutions. Such analyses are computationally intensive, especially when the pattern of relationships among a large number of entities is being sought. This thesis introduces two novel algorithms for the inference of large trees; one is applicable to the likelihood framework, the other to the Bayesian framework. Both approaches rely on the notion of a multi-modal tree 'landscape' through which inferential algorithms traverse. Using sampling techniques, the landscape can be perturbed sequentially, such that local optima can be evaded. The algorithms find good solutions in reasonable time, as demonstrated using real and simulated data sets. An example of large phylogeny inference is presented in the form of a novel estimate of Primate phylogeny- the largest estimate for this Order to date. The phylogeny is based on previously published smaller phylogenies, and hence serves as a summary of the present state of Primate phylogeny. In addition to this 'supertree's' topology, composite estimates of divergence are provided also. These estimates are based on multiple, clock-like genes combined using a novel approach presented here. Handling sets of trees and sequences poses practical problems in terms of conversion of data and the interoperation between computer programs. The thesis therefore concludes with a chapter discussing suitable data structures and programming patterns for phylogenetics. The appendix discusses an implementation of some of these concepts in an object-oriented application programming interface.

From Observations to Optimal Phylogenetic Trees

Author : Pablo A. Goloboff
Publisher : CRC Press
ISBN 13 : 1000550036
Total Pages : 299 pages
Book Rating : 4.0/5 (5 download)

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Book Synopsis From Observations to Optimal Phylogenetic Trees by : Pablo A. Goloboff

Download or read book From Observations to Optimal Phylogenetic Trees written by Pablo A. Goloboff and published by CRC Press. This book was released on 2022-07-22 with total page 299 pages. Available in PDF, EPUB and Kindle. Book excerpt: Taxonomists specializing in different groups once based phylogenetic analysis only on morphological data; molecular data was used more rarely. Although molecular systematics is routine today, the use of morphological data continues to be important, especially for phylogenetic placement of many taxa known only from fossils and rare or difficult to collect species. In addition, morphological analyses help identify potential biases in molecular analyses. And finally, scenarios with respect to morphology continue to motivate biologists: the beauty of a cheetah or a baobab does not lie in their DNA sequence, but instead on what they are and do! This book is an up-to-date revision of methods and principles of phylogenetic analysis of morphological data. It is also a general guide for using the computer program TNT in the analysis of such data. The book covers the main aspects of phylogenetic analysis and general methods to compare classifications derived from molecules and morphology. The basic aspects of molecular analysis are covered only as needed to highlight the differences with methods and assumptions for analysis of morphological datasets.

Phylogenetic Analysis of DNA Sequences

Author : Michael M. Miyamoto
Publisher : Oxford University Press, USA
ISBN 13 : 0195066987
Total Pages : 369 pages
Book Rating : 4.1/5 (95 download)

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Book Synopsis Phylogenetic Analysis of DNA Sequences by : Michael M. Miyamoto

Download or read book Phylogenetic Analysis of DNA Sequences written by Michael M. Miyamoto and published by Oxford University Press, USA. This book was released on 1991 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: With increasing frequency, systematic and evolutionary biologists have turned to the techniques of molecular biology to complement their traditional morphological and anatomical approaches to questions of historical relationship and descent among groups of animals and plants. In particular, the comparative analysis of DNA sequences is becoming a common and important focus of research attention today. This volume surveys the emerging field of molecular systematics of DNA sequences by focusing on the following topics: DNA sequence data acquisition; phylogenetic inference; congruence and consensus problems; limitations of molecular data; and integration of molecular and morphological data sets. The volume takes its inspiration from a major symposium sponsored by the American Society of Zoologists and the Society of Systematic Zoology in December, 1989.

Classification, Data Analysis, and Knowledge Organization

Author : Hans-Hermann Bock
Publisher : Springer Science & Business Media
ISBN 13 : 3642763073
Total Pages : 404 pages
Book Rating : 4.6/5 (427 download)

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Book Synopsis Classification, Data Analysis, and Knowledge Organization by : Hans-Hermann Bock

Download or read book Classification, Data Analysis, and Knowledge Organization written by Hans-Hermann Bock and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 404 pages. Available in PDF, EPUB and Kindle. Book excerpt: In science, industry, public administration and documentation centers large amounts of data and information are collected which must be analyzed, ordered, visualized, classified and stored efficiently in order to be useful for practical applications. This volume contains 50 selected theoretical and applied papers presenting a wealth of new and innovative ideas, methods, models and systems which can be used for this purpose. It combines papers and strategies from two main streams of research in an interdisciplinary, dynamic and exciting way: On the one hand, mathematical and statistical methods are described which allow a quantitative analysis of data, provide strategies for classifying objects or making exploratory searches for interesting structures, and give ways to make comprehensive graphical displays of large arrays of data. On the other hand, papers related to information sciences, informatics and data bank systems provide powerful tools for representing, modelling, storing and retrieving facts, data and knowledge characterized by qualitative descriptors, semantic relations, or linguistic concepts. The integration of both fields and a special part on applied problems from biology, medicine, archeology, industry and administration assure that this volume will be informative and useful for theory and practice.