Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R

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 ...

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 9781461417439

Category: Science

Page: 386

View: 387

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.
Categories: Science

Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R

This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language.

Author: Emmanuel Paradis

Publisher: Springer

ISBN: 0387512721

Category: Science

Page: 211

View: 971

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.
Categories: Science

Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R

We may recall that in R, all actions are done on objects stored in the active memory of the computer. Consequently, the classes described above are not designed to be new tree file formats, but rather to handle and analyze phylogenetic ...

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 9780387351001

Category: Science

Page: 211

View: 373

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.
Categories: Science

Bayesian Evolutionary Analysis with BEAST

Bayesian Evolutionary Analysis with BEAST

These are just a few of the questions answered in this comprehensive overview of Bayesian approaches to phylogenetics.

Author: Alexei J. Drummond

Publisher: Cambridge University Press

ISBN: 9781316298343

Category: Science

Page:

View: 310

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.
Categories: Science

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Methods Ecol Evol 3:743–756 Orme D, Freckleton R, Thomas G, Petzoldt T, Fritz S, Isaac N, Pearse W (2012) caper: comparative analysis of phylogenetics and evolution in R. http://CRAN.R-project.org/ package=caper Pagel MD (1992) A method ...

Author: László Zsolt Garamszegi

Publisher: Springer

ISBN: 9783662435502

Category: Science

Page: 552

View: 749

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.
Categories: Science

Phylogenetic Diversity

Phylogenetic Diversity

Am Nat 101:377–385 Maddison WP Maddison DR (2011) Mesquite: a modular system for evolutionary analysis. ... Analysis of phylogenetics and evolution with R. Springer, New York Redding DW, Mooers AO (2006) Incorporating evolutionary ...

Author: Rosa A. Scherson

Publisher: Springer

ISBN: 9783319931456

Category: Science

Page: 217

View: 726

“Biodiversity” refers to the variety of life. It is now agreed that there is a “biodiversity crisis”, corresponding to extinction rates of species that may be 1000 times what is thought to be “normal”. Biodiversity science has a higher profile than ever, with the new Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services involving more than 120 countries and 1000s of scientists. At the same time, the discipline is re-evaluating its foundations – including its philosophy and even core definitions. The value of biodiversity is being debated. In this context, the tree of life (“phylogeny”) is emerging as an important way to look at biodiversity, with relevance cutting across current areas of concern – from the question of resilience within ecosystems, to conservation priorities for globally threatened species – while capturing the values of biodiversity that have been hard to quantify, including resilience and maintaining options for future generations. This increased appreciation of the importance of conserving “phylogenetic diversity”, from microbial communities in the human gut to global threatened species, has inevitably resulted in an explosion of new indices, methods, and case studies. This book recognizes and responds to the timely opportunity for synthesis and sharing experiences in practical applications. The book recognizes that the challenge of finding a synthesis, and building shared concepts and a shared toolbox, requires both an appreciation of the past and a look into the future. Thus, the book is organized as a flow from history, concepts and philosophy, through to methods and tools, and followed by selected case studies. A positive vision and plan of action emerges from these chapters, that includes coping with inevitable uncertainties, effectively communicating the importance of this “evolutionary heritage” to the public and to policy-makers, and ultimately contributing to biodiversity conservation policy from local to global scales.
Categories: Science

Encyclopedia of Animal Behavior

Encyclopedia of Animal Behavior

Tempo and mode in evolution: Phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology 15, 899–910. Blomberg, S.P., Garland ... Caper: comparative analyses of phylogenetics and evolution in R. Pagel, M., ...

Author:

Publisher: Academic Press

ISBN: 9780128132524

Category: Science

Page: 3048

View: 622

Encyclopedia of Animal Behavior, Second Edition, the latest update since the 2010 release, builds upon the solid foundation established in the first edition. Updated sections include Host-parasite interactions, Vertebrate social behavior, and the introduction of ‘overview essays’ that boost the book's comprehensive detail. The structure for the work is modified to accommodate a better grouping of subjects. Some chapters have been reshuffled, with section headings combined or modified. Represents a one-stop resource for scientifically reliable information on animal behavior Provides comparative approaches, including the perspective of evolutionary biologists, physiologists, endocrinologists, neuroscientists and psychologists Includes multimedia features in the online version that offer accessible tools to readers looking to deepen their understanding
Categories: Science

Multivariate Analysis of Ecological Data with ade4

Multivariate Analysis of Ecological Data with ade4

Biometrics 62:471–477 Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20:289–290 Pavoine S, Bailly X (2007) New analysis for consistency among markers in the study of ...

Author: Jean Thioulouse

Publisher: Springer

ISBN: 9781493988501

Category: Medical

Page: 329

View: 359

This book introduces the ade4 package for R which provides multivariate methods for the analysis of ecological data. It is implemented around the mathematical concept of the duality diagram, and provides a unified framework for multivariate analysis. The authors offer a detailed presentation of the theoretical framework of the duality diagram and also of its application to real-world ecological problems. These two goals may seem contradictory, as they concern two separate groups of scientists, namely statisticians and ecologists. However, statistical ecology has become a scientific discipline of its own, and the good use of multivariate data analysis methods by ecologists implies a fair knowledge of the mathematical properties of these methods. The organization of the book is based on ecological questions, but these questions correspond to particular classes of data analysis methods. The first chapters present both usual and multiway data analysis methods. Further chapters are dedicated for example to the analysis of spatial data, of phylogenetic structures, and of biodiversity patterns. One chapter deals with multivariate data analysis graphs. In each chapter, the basic mathematical definitions of the methods and the outputs of the R functions available in ade4 are detailed in two different boxes. The text of the book itself can be read independently from these boxes. Thus the book offers the opportunity to find information about the ecological situation from which a question raises alongside the mathematical properties of methods that can be applied to answer this question, as well as the details of software outputs. Each example and all the graphs in this book come with executable R code.
Categories: Medical

Stick Insect Research in the Era of Genomics Exploring the Evolution of a Mesodiverse Insect Order

Stick Insect Research in the Era of Genomics  Exploring the Evolution of a Mesodiverse Insect Order

The caper package: comparative analysis of phylogenetics and evolution in R. R Package Version 5. Pagel, M. (1997). Inferring evolutionary processes from phylogenies. Zool. Scr. 26, 331–348. doi: 10.1111/j.1463-6409.1997.tb00423.x Pagel ...

Author: Sven Bradler

Publisher: Frontiers Media SA

ISBN: 9782889663712

Category: Science

Page:

View: 736

Categories: Science

Biotic Evolution and Environmental Change in Southeast Asia

Biotic Evolution and Environmental Change in Southeast Asia

Paralogy in cladistic biogeography and analysis ofparalogy-free subtrees. American Museum Novitates, 3167, 1-58. Paradis, E. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-90.

Author: David Gower

Publisher: Cambridge University Press

ISBN: 9781107001305

Category: Nature

Page: 475

View: 186

Authoritative reviews and focused case studies on the history and future of the fauna and flora of Southeast Asia.
Categories: Nature

Numerical Ecology with R

Numerical Ecology with R

R package version 0.2-6/r77. http://r-forge.r-project.org/projects/sedar/(2010) ape – Version used: 2.5-3 Paradis, E., Claude, J. and Strimmer, K.: APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290 ...

Author: Daniel Borcard

Publisher: Springer Science & Business Media

ISBN: 144197976X

Category: Medical

Page: 306

View: 766

Numerical Ecology with R provides a long-awaited bridge between a textbook in Numerical Ecology and the implementation of this discipline in the R language. After short theoretical overviews, the authors accompany the users through the exploration of the methods by means of applied and extensively commented examples. Users are invited to use this book as a teaching companion at the computer. The travel starts with exploratory approaches, proceeds with the construction of association matrices, then addresses three families of methods: clustering, unconstrained and canonical ordination, and spatial analysis. All the necessary data files, the scripts used in the chapters, as well as the extra R functions and packages written by the authors, can be downloaded from a web page accessible through the Springer web site(http://adn.biol.umontreal.ca/~numericalecology/numecolR/). This book is aimed at professional researchers, practitioners, graduate students and teachers in ecology, environmental science and engineering, and in related fields such as oceanography, molecular ecology, agriculture and soil science, who already have a background in general and multivariate statistics and wish to apply this knowledge to their data using the R language, as well as people willing to accompany their disciplinary learning with practical applications. People from other fields (e.g. geology, geography, paleoecology, phylogenetics, anthropology, the social and education sciences, etc.) may also benefit from the materials presented in this book. The three authors teach numerical ecology, both theoretical and practical, to a wide array of audiences, in regular courses in their Universities and in short courses given around the world. Daniel Borcard is lecturer of Biostatistics and Ecology and researcher in Numerical Ecology at Université de Montréal, Québec, Canada. François Gillet is professor of Community Ecology and Ecological Modelling at Université de Franche-Comté, Besançon, France. Pierre Legendre is professor of Quantitative Biology and Ecology at Université de Montréal, Fellow of the Royal Society of Canada, and ISI Highly Cited Researcher in Ecology/Environment.
Categories: Medical

Ecological and Evolutionary Aspects of Complex Relations between Micro and Macroparasites and their Wild Animal Hosts

Ecological and Evolutionary Aspects of Complex Relations between Micro  and Macroparasites and their Wild Animal Hosts

Network analysis of host–virus communities in bats and rodents reveals determinants of cross-species transmission. Ecol. Lett. ... APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290.

Author: Serge Morand

Publisher: Frontiers Media SA

ISBN: 9782889634835

Category:

Page:

View: 762

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Temporal Patterns and Mechanisms of Biodiversity Across Scales in East Asia

Temporal Patterns and Mechanisms of Biodiversity Across Scales in East Asia

Plasticity and evolution in drought avoidance and escape in the annual plant Brassica rapa. New Phytol. 190, 249–257. doi: 10.1111/j.1469-8137 ... Caper: Comparative Analysis of Phylogenetics and Evolution in R. R package version 1.0.1.

Author: Zehao Shen

Publisher: Frontiers Media SA

ISBN: 9782889710805

Category: Science

Page:

View: 110

Categories: Science

The Past and the Future of Human Immunity Under Viral Evolutionary Pressure

The Past and the Future of Human Immunity Under Viral Evolutionary Pressure

(2005) 79:6325–37. doi:10.1128/JVI.79.10.6325-6337.2005 Belshaw R, Katzourakis A, Paces J, Burt A, Tristem M. High copy number in ... (2017) 25:49–58. doi:10.1016/j.coviro.2017.07.001 Paradis E. Analysis of Phylogenetics and Evolution ...

Author: Gkikas Magiorkinis

Publisher: Frontiers Media SA

ISBN: 9782889632299

Category:

Page:

View: 575

There is a long-standing evolutionary battle between viruses and their hosts that continues to be waged. The evidence of this conflict can be found on both sides, with the human immune system being responsive to new viral challenges and viruses having developed often sophisticated countermeasures. The “arms race” between viruses and hosts can be thought as an example of the “Red Queen” race, an evolutionary hypothesis inspired from the dialogue of Alice with the Red Queen in Lewis Carroll’s “Through the Looking-Glass”. At the same time, viruses have a minimal genomic content as they have evolved to hitchhike biological machinery of their hosts (or other co-infecting viruses). The minimalistic viral genome could be thought as the result of a “Black Queen” evolution, a theory inspired from the card game Heart, where the winner is the one with the fewest points at the end. The effects of this arms race are evident in the evolution of the human immune system. This system is capable of responding to diverse viral challenges, utilizing both the ancient innate immune system and the more recently evolved adaptive immune system of jawed vertebrates. It is now well-known that the two systems are linked, with innate immunity hypothesized to have provided raw material for the emergence of the adaptive immune response. The adaptive immune response comprises several protein families (including B and T cell receptors, MHC and KIR proteins, for example) that are encoded by complex and variable genomic regions. This complexity enables for responsive genetic changes to occur in immune cells, such as the ability of genomic hypervariable regions in B cells to recombine in order to produce more specific antibodies. Indeed, the human immune system is thought to be continually evolving via various mechanisms such as changes in the genes encoding immune receptors and the regulatory sequences that control their expression. For example, there is some evidence that exogenous viral infections can alter the expression of endogenous retroviruses, some of which contribute to the immune response. Viral countermeasures can include encoding decoy receptors for the signalling molecules of the immune response, altering the gene expression of adaptive immune cells during chronic infection or using host enzymes to facilitate viral immune escape. As the articles herein show, the immune system continues to be challenged by viral infections and these challenges continue to shape how the immune system combats pathogens, thus viruses and human immunity are continuously part of “Red and Black Queen” evolutionary dynamics. We had the pleasure of working with Jonas Blomberg as a reviewer during the course of the Research Topic and his untimely passing was a great loss. Prof. Blomberg made significant contributions, including to the nomenclature of endogenous retroviruses (ERVs), the evolution and characterization of specific human ERV (HERV) and the contribution of ERVs to diseases such as cancer. It is with great respect for his contributions to the ERV field that we dedicate this eBook to his memory.
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Animal Mediated Dispersal in Understudied Systems

Animal Mediated Dispersal in Understudied Systems

Lizards in an Evolutionary Tree: Ecology and Adaptive Radiation of Anoles. Berkeley, CA: University of California Press. ... The Caper Package: Comparative Analysis of Phylogenetics and Evolution in R. R package, v. 1.0.1 (2018).

Author: Casper H. A. Van Leeuwen

Publisher: Frontiers Media SA

ISBN: 9782889634774

Category:

Page:

View: 744

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Estimating Species Trees

Estimating Species Trees

Evolution of genes and genomes on the Drosophila phylogeny. ... The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? ... Ape: analyses of phylogenetics and evolution in R language.

Author: L. Lacey Knowles

Publisher: John Wiley and Sons

ISBN: 9781118126028

Category: Science

Page: 232

View: 252

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.
Categories: Science

Bioinformatics Sequences Structures Phylogeny

Bioinformatics  Sequences  Structures  Phylogeny

This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis.

Author: Asheesh Shanker

Publisher: Springer

ISBN: 9789811315626

Category: Science

Page: 402

View: 447

This book provides a comprehensive overview of the concepts and approaches used for sequence, structure, and phylogenetic analysis. Starting with an introduction to the subject and intellectual property protection for bioinformatics, it guides readers through the latest sequencing technologies, sequence analysis, genomic variations, metagenomics, epigenomics, molecular evolution and phylogenetics, structural bioinformatics, protein folding, structure analysis and validation, drug discovery, reverse vaccinology, machine learning, application of R programming in biological data analysis, and the use of Linux in handling large data files.
Categories: Science

Mycoheterotrophy

Mycoheterotrophy

New Phytol 184:668–681 Matthews KG, Dunne N, York E, Struwe L (2009) A phylogenetic analysis and taxonomic ... Am J Bot 91:1437–1445 Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language.

Author: Vincent Merckx

Publisher: Springer Science & Business Media

ISBN: 9781461452096

Category: Science

Page: 356

View: 553

Over the course of evolution, several plant lineages have found ways to obtain water, minerals, and carbohydrates from fungi. Some plants are able exploit fungi to such an extent that they lose the need for photosynthesis. The ability of a plant to live on fungal carbon is known as mycoheterotrophy. This intriguing process has fascinated botanists for centuries, yet many aspects of mycoheterotrophy have remained elusive for a long time. Mycoheterotrophy: The Biology of Plants Living on Fungi explores the biology of mycoheterotrophs, offering general insights into their ecology, diversity, and evolution. Written by renowned experts in the field and bolstered with lavish illustrations and photographs, this volume provides a thematic overview of different aspects of mycoheterotrophy. Comprehensive and readily accessible, Mycoheterotrophy: The Biology of Plants Living on Fungi is a valuable resource for researchers and students who are interested in the process of mycoheterotrophy.
Categories: Science

Microbial Taxonomy Phylogeny and Biodiversity

Microbial Taxonomy  Phylogeny and Biodiversity

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. ... NbClust: an R package for determining the relevant number of clusters in a data set. J. Stat. Softw.

Author: Jesús L. Romalde

Publisher: Frontiers Media SA

ISBN: 9782889630509

Category:

Page: 375

View: 992

The great diversity of microbial life is the remaining major reservoir of unknown biological diversity on earth. To understand this vast, but largely unperceived diversity with its untapped genetic, enzymatic and industrial potential, microbial systematics is undergoing a revolutionary change in its approach to describe novel taxa based on genomic/envirogenomic information. The characterization of an organism is no longer bounded by methodological barriers, and it is now possible to fully sequence the whole genome of a strain to study individual genes, or to examine the genetic information by using different techniques. In fact, application of genomics is helping not only to provide a better understanding of the boundaries of genera and higher levels of classification, but also to refine our definition of the species concept. In addition, increased understanding of phylogeny is allowing to predict the genetic potential of microorganisms for biotechnological applications and adaptation to environmental changes. The present Research Topic on “Microbial Taxonomy, Phylogeny and Biodiversity” compiles a collection of papers covering the use of genomic sequence data in microbial taxonomy and systematics, including evolutionary relatedness of microorganisms; application of comparative genomics in systematic studies; or metagenomic approaches for biodiversity studies. We hope that this eBook incentives and encourages researchers for future discussions on microbial taxonomy and phylogenetics.
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