Phylogenetic Comparative Methods In R

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Phylogenetic Comparative Methods in R

Liam J. Revell,Luke J. Harmon
Phylogenetic Comparative Methods in R Book PDF

Author : Liam J. Revell,Luke J. Harmon
Publisher : Princeton University Press
Page : 440 pages
File Size : 55,5 Mb
Release : 2022-09-06
Category : Science
ISBN : 9780691219035

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Phylogenetic Comparative Methods in R by Liam J. Revell,Luke J. Harmon Pdf

An authoritative introduction to the latest comparative methods in evolutionary biology Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life. Covers every major method of modern phylogenetic comparative analysis in RExplains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualizationFeatures a wealth of exercises and challenge problemsServes as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areasWritten by two of today’s leading developers of phylogenetic comparative methods

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

László Zsolt Garamszegi
Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology Book PDF

Author : László Zsolt Garamszegi
Publisher : Springer
Page : 552 pages
File Size : 45,5 Mb
Release : 2014-07-29
Category : Science
ISBN : 9783662435502

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Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology by László Zsolt Garamszegi Pdf

Phylogenetic 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.

Analysis of Phylogenetics and Evolution with R

Emmanuel Paradis
Analysis of Phylogenetics and Evolution with R Book PDF

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 221 pages
File Size : 50,5 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.

Phylogenetic Comparative Methods

Luke J. Harmon
Phylogenetic Comparative Methods Book PDF

Author : Luke J. Harmon
Publisher : Unknown
Page : 286 pages
File Size : 41,5 Mb
Release : 2018-05-23
Category : Electronic
ISBN : 171958446X

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Phylogenetic Comparative Methods by Luke J. Harmon Pdf

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

Analysis of Phylogenetics and Evolution with R

Emmanuel Paradis
Analysis of Phylogenetics and Evolution with R Book PDF

Author : Emmanuel Paradis
Publisher : Springer Science & Business Media
Page : 401 pages
File Size : 43,8 Mb
Release : 2011-11-06
Category : Science
ISBN : 9781461417439

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Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis Pdf

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.

Functional and Phylogenetic Ecology in R

Nathan G. Swenson
Functional and Phylogenetic Ecology in R Book PDF

Author : Nathan G. Swenson
Publisher : Springer Science & Business Media
Page : 217 pages
File Size : 46,5 Mb
Release : 2014-03-26
Category : Computers
ISBN : 9781461495420

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Functional and Phylogenetic Ecology in R by Nathan G. Swenson Pdf

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.

Phylogenetic Comparative Methods in R

Liam J. Revell,Luke J. Harmon
Phylogenetic Comparative Methods in R Book PDF

Author : Liam J. Revell,Luke J. Harmon
Publisher : Princeton University Press
Page : 441 pages
File Size : 40,5 Mb
Release : 2022-07-12
Category : Science
ISBN : 9780691219042

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Phylogenetic Comparative Methods in R by Liam J. Revell,Luke J. Harmon Pdf

An authoritative introduction to the latest comparative methods in evolutionary biology Phylogenetic comparative methods are a suite of statistical approaches that enable biologists to analyze and better understand the evolutionary tree of life, and shed vital new light on patterns of divergence and common ancestry among all species on Earth. This textbook shows how to carry out phylogenetic comparative analyses in the R statistical computing environment. Liam Revell and Luke Harmon provide an incisive conceptual overview of each method along with worked examples using real data and challenge problems that encourage students to learn by doing. By working through this book, students will gain a solid foundation in these methods and develop the skills they need to interpret patterns in the tree of life. Covers every major method of modern phylogenetic comparative analysis in R Explains the basics of R and discusses topics such as trait evolution, diversification, trait-dependent diversification, biogeography, and visualization Features a wealth of exercises and challenge problems Serves as an invaluable resource for students and researchers, with applications in ecology, evolution, anthropology, disease transmission, conservation biology, and a host of other areas Written by two of today’s leading developers of phylogenetic comparative methods

The Comparative Approach in Evolutionary Anthropology and Biology

Charles L. Nunn
The Comparative Approach in Evolutionary Anthropology and Biology Book PDF

Author : Charles L. Nunn
Publisher : University of Chicago Press
Page : 392 pages
File Size : 53,9 Mb
Release : 2011-11-30
Category : Science
ISBN : 9780226608983

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The Comparative Approach in Evolutionary Anthropology and Biology by Charles L. Nunn Pdf

And when new fossils are found, such as those of the tiny humans of Flores, scientists compare these remains to other fossils and contemporary humans.

Analysis of Phylogenetics and Evolution with R

Emmanuel Paradis
Analysis of Phylogenetics and Evolution with R Book PDF

Author : Emmanuel Paradis
Publisher : Springer
Page : 0 pages
File Size : 53,9 Mb
Release : 2008-11-01
Category : Science
ISBN : 0387512721

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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.

Handbook of Trait-Based Ecology

Francesco de Bello,Carlos P. Carmona,André T. C. Dias,Lars Götzenberger,Marco Moretti,Matty P. Berg
Handbook of Trait Based Ecology Book PDF

Author : Francesco de Bello,Carlos P. Carmona,André T. C. Dias,Lars Götzenberger,Marco Moretti,Matty P. Berg
Publisher : Cambridge University Press
Page : 311 pages
File Size : 49,6 Mb
Release : 2021-03-11
Category : Nature
ISBN : 9781108472913

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Handbook of Trait-Based Ecology by Francesco de Bello,Carlos P. Carmona,André T. C. Dias,Lars Götzenberger,Marco Moretti,Matty P. Berg Pdf

Trait-based ecology is rapidly expanding. This comprehensive and accessible guide covers the main concepts and tools in functional ecology.

Bayesian Phylogenetics

Ming-Hui Chen,Lynn Kuo,Paul O. Lewis
Bayesian Phylogenetics Book PDF

Author : Ming-Hui Chen,Lynn Kuo,Paul O. Lewis
Publisher : CRC Press
Page : 398 pages
File Size : 50,5 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.

Parasite Diversity and Diversification

Serge Morand,Boris R. Krasnov,D. Timothy J. Littlewood
Parasite Diversity and Diversification Book PDF

Author : Serge Morand,Boris R. Krasnov,D. Timothy J. Littlewood
Publisher : Cambridge University Press
Page : 503 pages
File Size : 40,7 Mb
Release : 2015-02-26
Category : Medical
ISBN : 9781107037656

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Parasite Diversity and Diversification by Serge Morand,Boris R. Krasnov,D. Timothy J. Littlewood Pdf

By joining phylogenetics and evolutionary ecology, this book explores the patterns of parasite diversity while revealing diversification processes.

Tree Thinking: An Introduction to Phylogenetic Biology

David A. Baum,Stacey D. Smith
Tree Thinking An Introduction to Phylogenetic Biology Book PDF

Author : David A. Baum,Stacey D. Smith
Publisher : Roberts
Page : 0 pages
File Size : 46,6 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.

The Phylogenetic Handbook

Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey
The Phylogenetic Handbook Book PDF

Author : Marco Salemi,Anne-Mieke Vandamme,Philippe Lemey
Publisher : Cambridge University Press
Page : 750 pages
File Size : 51,8 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.

Molecular Evolution

Ziheng Yang
Molecular Evolution Book PDF

Author : Ziheng Yang
Publisher : Oxford University Press
Page : 509 pages
File Size : 44,9 Mb
Release : 2014
Category : Science
ISBN : 9780199602605

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Molecular Evolution by Ziheng Yang Pdf

This book presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. The book offers numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative.