Bayesian Evolutionary Analysis with BEAST

Author: Alexei J. Drummond,Remco R. Bouckaert

Publisher: Cambridge University Press

ISBN: 1107019656

Category: Science

Page: 260

View: 2592

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Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.

Bayesian Evolutionary Analysis with BEAST

Author: Alexei J. Drummond,Remco R. Bouckaert

Publisher: Cambridge University Press

ISBN: 1316298345

Category: Science

Page: N.A

View: 7521

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What are the models used in phylogenetic analysis and what exactly is involved in Bayesian evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you choose and apply these models, which parameterisations and priors make sense, and how can you diagnose Bayesian MCMC when things go wrong? These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics. This practical guide: • Addresses the theoretical aspects of the field • Advises on how to prepare and perform phylogenetic analysis • Helps with interpreting analyses and visualisation of phylogenies • Describes the software architecture • Helps developing BEAST 2.2 extensions to allow these models to be extended further. With an accompanying website providing example files and tutorials (http://beast2.org/), this one-stop reference to applying the latest phylogenetic models in BEAST 2 will provide essential guidance for all users – from those using phylogenetic tools, to computational biologists and Bayesian statisticians.

Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 1461417430

Category: Science

Page: 386

View: 5220

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The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. 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: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. 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.

Molecular Evolution and Phylogenetics

Author: Masatoshi Nei,Sudhir Kumar

Publisher: Oxford University Press

ISBN: 0199881227

Category: Science

Page: 352

View: 2564

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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.

Bayesian Phylogenetics

Methods, Algorithms, and Applications

Author: Ming-Hui Chen,Lynn Kuo,Paul O. Lewis

Publisher: CRC Press

ISBN: 1466500794

Category: Mathematics

Page: 396

View: 2508

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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.

Phylogenetics

Theory and Practice of Phylogenetic Systematics

Author: E. O. Wiley,Bruce S. Lieberman

Publisher: John Wiley & Sons

ISBN: 1118017870

Category: Science

Page: 424

View: 783

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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.

Functional and Phylogenetic Ecology in R

Author: Nathan G. Swenson

Publisher: Springer Science & Business Media

ISBN: 1461495423

Category: Computers

Page: 212

View: 7781

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Functional and Phylogenetic Ecology in R is designed to teach readers to use R for phylogenetic and functional trait analyses. Over the past decade, a dizzying array of tools and methods were generated to incorporate phylogenetic and functional information into traditional ecological analyses. Increasingly these tools are implemented in R, thus greatly expanding their impact. Researchers getting started in R can use this volume as a step-by-step entryway into phylogenetic and functional analyses for ecology in R. More advanced users will be able to use this volume as a quick reference to understand particular analyses. The volume begins with an introduction to the R environment and handling relevant data in R. Chapters then cover phylogenetic and functional metrics of biodiversity; null modeling and randomizations for phylogenetic and functional trait analyses; integrating phylogenetic and functional trait information; and interfacing the R environment with a popular C-based program. This book presents a unique approach through its focus on ecological analyses and not macroevolutionary analyses. The author provides his own code, so that the reader is guided through the computational steps to calculate the desired metrics. This guided approach simplifies the work of determining which package to use for any given analysis. Example datasets are shared to help readers practice, and readers can then quickly turn to their own datasets.

Inferring Phylogenies

Author: Joseph Felsenstein

Publisher: Sinauer Associates Incorporated

ISBN: 9780878931774

Category: Science

Page: 664

View: 2624

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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.

Molecular Evolution

A Statistical Approach

Author: Ziheng Yang

Publisher: Oxford University Press

ISBN: 0199602603

Category: Science

Page: 492

View: 2735

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"Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology."--back cover.

Phylogenetic Trees Made Easy

A How-To Manual

Author: Barry G. Hall

Publisher: Sinauer

ISBN: 9781605357102

Category: Science

Page: 310

View: 5409

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Phylogenetic Trees Made Easy, Fifth Edition leads the reader, step by step, through identifying and acquiring the sequences to be included in a tree, aligning the sequences, estimating the tree by one of several methods, and drawing the tree for presentation to an intended audience. Although aimed at molecular and cell biologists, who may not be familiar with phylogenetic or evolutionary theory, it also serves students who have a theoretical understanding of phylogenetics but need guidance in transitioning to a practical application of the methodology.

The Phylogenetic Handbook

A Practical Approach to Phylogenetic Analysis and Hypothesis Testing

Author: Philippe Lemey,Marco Salemi,Anne-Mieke Vandamme

Publisher: Cambridge University Press

ISBN: 9781139478618

Category: Science

Page: N.A

View: 2770

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The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.

Phylogenetic Comparative Methods

Learning from Trees

Author: Luke J. Harmon

Publisher: N.A

ISBN: 9781719584463

Category:

Page: 286

View: 9094

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An introduction to statistical analyses of phylogenetic trees using comparative methods.

Computational Molecular Evolution

Author: Ziheng Yang

Publisher: Oxford University Press

ISBN: 0198566999

Category: Medical

Page: 357

View: 6166

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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.

Estimating Species Trees

Practical and Theoretical Aspects

Author: L. Lacey Knowles,Laura S. Kubatko

Publisher: John Wiley & Sons

ISBN: 1118211405

Category: Science

Page: 232

View: 4974

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Recent computational and modeling advances have produced methods for estimating species trees directly, avoiding the problems and limitations of the traditional phylogenetic paradigm where an estimated gene tree is equated with the history of species divergence. The overarching goal of the volume is to increase the visibility and use of these new methods by the entire phylogenetic community by specifically addressing several challenges: (i) firm understanding of the theoretical underpinnings of the methodology, (ii) empirical examples demonstrating the utility of the methodology as well as its limitations, and (iii) attention to technical aspects involved in the actual software implementation of the methodology. As such, this volume will not only be poised to become the quintessential guide to training the next generation of researchers, but it will also be instrumental in ushering in a new phylogenetic paradigm for the 21st century.

The Phylogenetic Handbook

A Practical Approach to DNA and Protein Phylogeny

Author: Marco Salemi,Anne-Mieke Vandamme

Publisher: Cambridge University Press

ISBN: 9780521803908

Category: Computers

Page: 406

View: 4630

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Introduction to the theory and practice of phylogenetic analysis for molecular evolution students and professionals.

Evolutionary Analysis, Global Edition

Author: Scott Freeman,Jon C. Herron,Jason Hodin

Publisher: N.A

ISBN: 9781292061276

Category: Evolution

Page: 864

View: 2995

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For undergraduate courses in Evolution By presenting evolutionary biology as a dynamic, ongoing research effort and organizing discussions around questions, this best-selling text helps students think like scientists as they learn about evolution. The authors convey the excitement and logic of evolutionary science by introducing principles through recent and classical studies, and by emphasizing real-world applications. In the Fifth Edition, co-author Jon Herron takes the lead in streamlining and updating content to reflect key changes in the field. The design and art program have also been updated for enhanced clarity.

Darwin's Dangerous Idea

Evolution and the Meaning of Life

Author: Daniel C. Dennett

Publisher: Simon and Schuster

ISBN: 1439126291

Category: Science

Page: 592

View: 7495

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In a book that is both groundbreaking and accessible, Daniel C. Dennett, whom Chet Raymo of The Boston Globe calls "one of the most provocative thinkers on the planet," focuses his unerringly logical mind on the theory of natural selection, showing how Darwin's great idea transforms and illuminates our traditional view of humanity's place in the universe. Dennett vividly describes the theory itself and then extends Darwin's vision with impeccable arguments to their often surprising conclusions, challenging the views of some of the most famous scientists of our day.

Gene Genealogies, Variation and Evolution: A primer in coalescent theory

Author: Jotun Hein,Mikkel Schierup,Carsten Wiuf

Publisher: Oxford University Press, USA

ISBN: 9780191546150

Category:

Page: 296

View: 6408

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Authored by leading experts, this seminal text presents a straightforward and elementary account of coalescent theory, which is a central concept in the study of genetic sequence variation observed in a population. Rich in examples and illustrations it is ideal for a graduate course in statistics, population, molecular and medical genetics, bioscience and medicine, and for students studying the evolution of human population and disease. It is also an invaluable reference for bioscientists and statisticians in the pharmaceutical industry and academia - ;Coalescent theory is a central concept in the study of genetic sequence variation that probabilistically describes the genealogy relating the sampled sequences. In this text, besides fulfilling the glaring need for such a book, the authors present this theory in a straightforward and elementary manner and describe the statistical and computational methods used in modelling and analyzing genetic sequence variation. Rich in examples and illustrations the book covers basic concepts, complications arising from geographical structure and recombination before considering aspects of statistical inference based on these models. The book ends with chapters on Gene Mapping, which combines sequence variation data with phenotypic data (such as disease) to define areas of the genome where genes are responsible for the trait, and Human Evolution, a research area that is experiencing a renaissance due to the enormous amounts of data produced in molecular studies. Authored by leading experts, this seminal text presents a straightforward and elementary account of coalescent theory, which is a central concept in the study of genetic sequence variation observed in a population. It is highly suitable for a graduate course in statistics, population, molecular and medical genetics, bioscience and medicine and students studying the evolution of human population and disease, and will be an invaluable reference for bioscientists and statisticians in the pharmaceutical industry and academia - ;an excellent and timely book that should appeal to a variety of people in genetics and applied mathematics. - Professor Montgomery Slatkin (Berkeley);the authors are outstanding experts in the field, and the book is topical and timely. - Professor David Balding (Imperial College);Hein, Schierup and Wiuf have written the first general book on the coalescent. It is an engaging combination of clear mathematical derivation and real data examples. - Professor Joe Felsenstein (University of Washington)

Why Evolution is True

Author: Jerry A. Coyne

Publisher: OUP Oxford

ISBN: 019164384X

Category: Science

Page: 336

View: 7526

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For all the discussion in the media about creationism and 'Intelligent Design', virtually nothing has been said about the evidence in question - the evidence for evolution by natural selection. Yet, as this succinct and important book shows, that evidence is vast, varied, and magnificent, and drawn from many disparate fields of science. The very latest research is uncovering a stream of evidence revealing evolution in action - from the actual observation of a species splitting into two, to new fossil discoveries, to the deciphering of the evidence stored in our genome. Why Evolution is True weaves together the many threads of modern work in genetics, palaeontology, geology, molecular biology, anatomy, and development to demonstrate the 'indelible stamp' of the processes first proposed by Darwin. It is a crisp, lucid, and accessible statement that will leave no one with an open mind in any doubt about the truth of evolution.

Human Evolutionary Trees

Author: E. A. Thompson

Publisher: CUP Archive

ISBN: 9780521099455

Category: Science

Page: 158

View: 498

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Originally published in 1975, this book analyses the way in which inferences about the evolutionary history of human populations may be made from genetic data of modern populations. Problems of scientific inference arise in the interpretation of the model and its results and many points of interest in the theory of the foundations of inference are illustrated.