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 ...

Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer Science & Business Media

ISBN: 1461417430

Page: 386

View: 609

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.

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.

Analysis of Phylogenetics and Evolution with R

Author: Emmanuel Paradis

Publisher: Springer

ISBN: 9780387512723

Page: 211

View: 273

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.

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Proc Roy Soc Ser B 255:37–45 Paradis E (2012) Analysis of phylogenetics and Evolution with R, 2nd edn. Springer, New York Paradis E, Claude J, ...

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

Author: László Zsolt Garamszegi

Publisher: Springer

ISBN: 3662435500

Page: 552

View: 593

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.

Functional and Phylogenetic Ecology in R

The role of evolutionary processes in producing biodiversity patterns, ... Analysis of phylogenetics and evolution with R. New York: Springer.

Functional and Phylogenetic Ecology in R

Author: Nathan G. Swenson

Publisher: Springer Science & Business Media

ISBN: 1461495423

Page: 212

View: 324

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.

Bayesian Evolutionary Analysis with BEAST

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

Publisher: Cambridge University Press

ISBN: 1107019656

Page: 260

View: 654

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

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 ...

Multivariate Analysis of Ecological Data with ade4

Author: Jean Thioulouse

Publisher: Springer

ISBN: 1493988506

Page: 329

View: 944

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.

Biotic Evolution and Environmental Change in Southeast Asia

APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20, 289-90. Pfeil, B. E. and Crisp, M. D. (2008). The age and biogeography of ...

Biotic Evolution and Environmental Change in Southeast Asia

Author: David Gower

Publisher: Cambridge University Press

ISBN: 1107001307

Page: 475

View: 486

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

Computer Simulation and Data Analysis in Molecular Biology and Biophysics

Because of these capabilities, R can serve as your basic quantitative, statistical, ... Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis, ...

Computer Simulation and Data Analysis in Molecular Biology and Biophysics

Author: Victor Bloomfield

Publisher: Springer Science & Business Media

ISBN: 1441900837

Page: 321

View: 885

This book provides an introduction to two important aspects of modern bioch- istry, molecular biology, and biophysics: computer simulation and data analysis. My aim is to introduce the tools that will enable students to learn and use some f- damental methods to construct quantitative models of biological mechanisms, both deterministicandwithsomeelementsofrandomness;tolearnhowconceptsofpr- ability can help to understand important features of DNA sequences; and to apply a useful set of statistical methods to analysis of experimental data. The availability of very capable but inexpensive personal computers and software makes it possible to do such work at a much higher level, but in a much easier way, than ever before. TheExecutiveSummaryofthein?uential2003reportfromtheNationalAcademy of Sciences, “BIO 2010: Transforming Undergraduate Education for Future - search Biologists” [12], begins The interplay of the recombinant DNA, instrumentation, and digital revolutions has p- foundly transformed biological research. The con?uence of these three innovations has led to important discoveries, such as the mapping of the human genome. How biologists design, perform, and analyze experiments is changing swiftly. Biological concepts and models are becoming more quantitative, and biological research has become critically dependent on concepts and methods drawn from other scienti?c disciplines. The connections between the biological sciences and the physical sciences, mathematics, and computer science are rapidly becoming deeper and more extensive.

Numerical Ecology with R

Springer, New York (2007) References – R packages (in alphabetical order): The list ... K.: APE: analyses of phylogenetics and evolution in R language.

Numerical Ecology with R

Author: Daniel Borcard

Publisher: Springer Science & Business Media

ISBN: 9781441979766

Page: 306

View: 654

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.

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

Chuong EB, Elde NC, Feschotte C. Regulatory evolution of innate immunity through ... Strimmer K. APE: analyses of phylogenetics and evolution in R language.

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

Author: Gkikas Magiorkinis

Publisher: Frontiers Media SA

ISBN: 2889632296

Page:

View: 233

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.

Fitness Costs and Benefits of Female Song

The caper package: comparative analysis of phylogenetics and evolution in R. Available online at: http://cran.r-project.org/web/packages/ ...

Fitness Costs and Benefits of Female Song

Author: Michelle L. Hall

Publisher: Frontiers Media SA

ISBN: 2889452581

Page:

View: 753

Bird song, traditionally regarded as primarily a male trait, is in fact widespread among female songbirds and was probably present in the ancestor of modern songbirds (Odom et al 2014 Nature Communications). These recent findings challenge the view that sexual dimorphism in the expression and complexity of song is largely the outcome of sexual selection on males. It is now clear that understanding the evolution of bird song requires explaining variation within and among species in the expression and complexity of female song. To do this, we need a better understanding of the nature of variation in female song in different contexts and systems, as well as the fitness costs and benefits of variation in the expression and complexity of female song. This Research Topic draws together current research on female song with the goal of understanding the fitness costs and benefits of the diversity of female singing behaviour apparent among songbirds. It includes articles ranging from single-species studies investigating how female song varies with context and contrasts with male song, to comparative analyses exploring relationships between female song and ecological, social, and other factors, as well as opinion pieces.

Origin of Tropical Diversity From Clades to Communities

APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20, 289–290. doi:10.1093/bioinformatics/btg412 Phillips, O. L., Martinez, R. V., ...

Origin of Tropical Diversity  From Clades to Communities

Author: James Edward Richardson

Publisher: Frontiers Media SA

ISBN: 2889450503

Page:

View: 665

In this volume we aimed to assess progress in determining the processes by which current patterns of tropical biodiversity were established and are maintained. Tropical regions are highly species-rich and we present studies that have improved our understanding of the generation of that diversity at local, regional and global scales. We demonstrate how diverse fields from molecular phylogenetics, phylogeography, palaeontology and palaeoecology continue to improve our understanding of the natural history of the tropics.

Evolutionary Trajectories in Plant Associated Pseudomonas and Xanthomonas Strains

Phylogenetic. Analysis. Single gene evolution may be different from the evolution ... ClonalFrameML calculates R/theta, nu, and 1/delta, which represent the ...

Evolutionary Trajectories in Plant Associated Pseudomonas and Xanthomonas Strains

Author: Marco Scortichini

Publisher: Frontiers Media SA

ISBN: 288963700X

Page:

View: 665

The strict relationships between bacteria and plants represent one of the major facets of terrestrial ecology. Depending on the type of interaction and amount of metabolic advantage one organism can obtain from such relationships, these are classified as mutualistic, commensal or parasitic interactions. Within this context, Pseudomonas and Xanthomonas are bacterial genera with a worldwide spread, capable of establishing all of the above mentioned interactions with plants. Therefore, they represent good models for studying different lifestyles and, accordingly, deciphering distinct evolutionary trajectories followed by different lineages of a single genus to infect and/or to establish a mutualistic relationships with the plant. Some members of these two genera are regulated pests that are recognized as economically major threats for their host crop(s) both in temperate and tropical environments. Some Pseudomonas and Xanthomonas are key examples of different lifestyles (i.e., mesophyll or vessel-colonizing pathogens, epiphytic pathogens, plant growth-promoting rhizobacteria, non-pathogenic strains of recognized pathogenic species, etc). Refining our knowledge on the ecology and epidemiology of these bacterial groups, as well as deciphering their evolutionary dynamics are keys for understanding their contrasting lifestyles and consequently improving plant disease control. At the same time, insights on the activation of different plant defense mechanisms as challenged by the different repertoires of virulence factors displayed by pseudomonads and xanthomonads, would yield new achievements to reduce the threats they pose to cultivated and wild plant species. This Research Topic focuses on microbial and evolutionary ecology of plant associated Pseudomonas and Xanthomonas, as well as the genomic and molecular diversity of lineages and the virulence and fitness features involved in the interaction with the host-plant. Most of the literature available for this Research Topic has been performed for strains isolated in temperate zones. In line with the long-recognized high social and environmental impact of pests and pathogens in tropical countries, we have welcomed submissions of studies covering such situations for these areas. This Research Topic gathers high-quality contributions (Original Research, Methods, Protocols, Hypothesis & Theory, Reviews, Mini Reviews, Focused Reviews) and in order to promote complementary and original research approaches to improve our knowledge on pseudomonads and xanthomonads-host interactions and their control, it benefited from the scientific communities currently working on Pseudomonas and Xanthomonas such as the teams dealing with the Pseudomonas syringae species complex and the French Network on Xanthomonads (FNX).

Modern Data Science with R

... Analyses of Phylogenetics and Evolution. R package version 5.4-1. Pebesma, E. (2021). sf: Simple Features for R. R package version 0.9-7.

Modern Data Science with R

Author: Benjamin S. Baumer

Publisher: CRC Press

ISBN: 0429577508

Page: 650

View: 257

From a review of the first edition: "Modern Data Science with R... is rich with examples and is guided by a strong narrative voice. What’s more, it presents an organizing framework that makes a convincing argument that data science is a course distinct from applied statistics" (The American Statistician). Modern Data Science with R is a comprehensive data science textbook for undergraduates that incorporates statistical and computational thinking to solve real-world data problems. Rather than focus exclusively on case studies or programming syntax, this book illustrates how statistical programming in the state-of-the-art R/RStudio computing environment can be leveraged to extract meaningful information from a variety of data in the service of addressing compelling questions. The second edition is updated to reflect the growing influence of the tidyverse set of packages. All code in the book has been revised and styled to be more readable and easier to understand. New functionality from packages like sf, purrr, tidymodels, and tidytext is now integrated into the text. All chapters have been revised, and several have been split, re-organized, or re-imagined to meet the shifting landscape of best practice.

Numerical Ecology

The list provides, in alphabetic order, references for the R packages cited in the Software sections ... 2012. ape: Analyses of phylogenetics and evolution.

Numerical Ecology

Author: P. Legendre

Publisher: Elsevier

ISBN: 0444538682

Page: 990

View: 299

The book describes and discusses the numerical methods which are successfully being used for analysing ecological data, using a clear and comprehensive approach. These methods are derived from the fields of mathematical physics, parametric and nonparametric statistics, information theory, numerical taxonomy, archaeology, psychometry, sociometry, econometry and others. An updated, 3rd English edition of the most widely cited book on quantitative analysis of multivariate ecological data Relates ecological questions to methods of statistical analysis, with a clear description of complex numerical methods All methods are illustrated by examples from the ecological literature so that ecologists clearly see how to use the methods and approaches in their own research All calculations are available in R language functions

The Molecular Evolutionary Clock

Syst Biol 54:401–418 guide to Bayesian phylogenetic analysis. ... Rasnitsyn AP (2012a) A total-evidence phylogenetics and evolution in R language.

The Molecular Evolutionary Clock

Author: Simon Y. W. Ho

Publisher: Springer Nature

ISBN: 3030601811

Page: 249

View: 423

This book presents coverage of the principles and practice of molecular clocks, which have provided fascinating and unprecedented insights into the evolutionary timescale of life on earth. It begins by following the early development of the molecular evolutionary clock in the 1960s, and leads to the complex statistical approaches that are now used to analyse genome sequences. The chapters of this book have been contributed by leading experts in the field and address the important issues of evolutionary rates, molecular dating, and phylogenomic analysis. This is the first time that these different aspects of the molecular clock have been brought together in a single, comprehensive volume. It is an invaluable reference for students and researchers interested in evolutionary biology, genetic analysis, and genomic evolution.

Plant Systematics

Molecular Phylogenetics and Evolution 94:447-462. Felsenstein, J. 2003. ... Phybase, an R package for species tree analysis. Bioinformatics 26:962–963.

Plant Systematics

Author: Michael G. Simpson

Publisher: Academic Press

ISBN: 0128126299

Page: 774

View: 958

Plant Systematics, Third Edition, has made substantial contributions to plant systematics courses at the upper-undergraduate and first year graduate level, with the first edition winning The New York Botanical Garden's Henry Allan Gleason Award for outstanding recent publication in plant taxonomy, plant ecology or plant geography. This third edition continues to provide the basis for teaching an introduction to the morphology, evolution and classification of land plants. A foundation of the approach, methods, research goals, evidence and terminology of plant systematics are presented, along with the most recent knowledge of evolutionary relationships of plants and practical information vital to the field. In this new edition, the author includes greatly expanded treatments on families of flowering plants, as well as tropical trees (all with full-color plates), and an updated explanation of maximum likelihood and Bayesian inference algorithms. Chapters on morphology and plant nomenclature have also been enhanced with new material. Covers research developments in plant molecular biology Features clear, detailed cladograms, drawings and photos Includes major revisions to chapters on phylogenetic systematics and plant morphology

coscience

Today over 600 contributing packages are available for R users . The APE package ( Analyses of Phylogenetics and Evolution ; Paradis , Claude & Strimmer ...

  coscience

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