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
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.
This book integrates a wide variety of data analysis methods into a single and flexible interface: the R language.
Author: Emmanuel Paradis
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.
Author: László Zsolt GaramszegiPublish On: 2014-07-29
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, ...
Author: László Zsolt Garamszegi
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 (second edition). New York: Springer. Paradis, E. 2013. Molecular dating of phylogenies by likelihood ...
Author: Emmanuel Paradis
Publisher: CRC Press
Population Genomics With R presents a multidisciplinary approach to the analysis of population genomics. The methods treated cover a large number of topics from traditional population genetics to large-scale genomics with high-throughput sequencing data. Several dozen R packages are examined and integrated to provide a coherent software environment with a wide range of computational, statistical, and graphical tools. Small examples are used to illustrate the basics and published data are used as case studies. Readers are expected to have a basic knowledge of biology, genetics, and statistical inference methods. Graduate students and post-doctorate researchers will find resources to analyze their population genetic and genomic data as well as help them design new studies. The first four chapters review the basics of population genomics, data acquisition, and the use of R to store and manipulate genomic data. Chapter 5 treats the exploration of genomic data, an important issue when analysing large data sets. The other five chapters cover linkage disequilibrium, population genomic structure, geographical structure, past demographic events, and natural selection. These chapters include supervised and unsupervised methods, admixture analysis, an in-depth treatment of multivariate methods, and advice on how to handle GIS data. The analysis of natural selection, a traditional issue in evolutionary biology, has known a revival with modern population genomic data. All chapters include exercises. Supplemental materials are available on-line (http://ape-package.ird.fr/PGR.html).
Kembel SW, Hubbell SP (2006) The phylogenetic structure of a neotropical forest tree community ... Analysis of phylogenetics and evolution with R. Springer, ...
Author: Rosa A. Scherson
“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.
APE: Analyses of phylogenetics and evolution in R language. ... A phylogenetic analysis of body size evolution and biogeography in chuckwallas (Sauromalus) ...
Author: Brian I. Crother
Publisher: CRC Press
This book is a thought-provoking assessment of assumptions inhibiting progress in comparative biology. The volume is inspired by a list generated years earlier by Donn Rosen, one of the most influential, innovative and productive comparative biologists of the latter 20th century. His list has assumed almost legendary status among comparative evolutionary biologists. Surprisingly many of the obstructing assumptions implicated by Rosen remain relevant today. Any comparative biologist hoping to avoid such assumptions in their own research will benefit from this introspective volume.
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 ...
Author: Jean Thioulouse
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.
Because of these capabilities, R can serve as your basic quantitative, statistical, ... Analysis of Phylogenetics and Evolution with R by Emmanuel Paradis, ...
Author: Victor Bloomfield
Publisher: Springer Science & Business Media
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” , 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.
Springer, New York (2007) References – R packages (in alphabetical order): The list ... K.: APE: analyses of phylogenetics and evolution in R language.
Author: Daniel Borcard
Publisher: Springer Science & Business Media
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.
Chuong EB, Elde NC, Feschotte C. Regulatory evolution of innate immunity through ... Strimmer K. APE: analyses of phylogenetics and evolution in R language.
Author: Gkikas Magiorkinis
Publisher: Frontiers Media SA
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.
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
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.
A branch-heterogeneous model of protein evolution for efficient inference of ancestral ... Ape: Analyses of phylogenetics and evolution in R language.
Publisher: Academic Press
Encyclopedia of Evolutionary Biology is the definitive go-to reference in the field of evolutionary biology. It provides a fully comprehensive review of the field in an easy to search structure. Under the collective leadership of fifteen distinguished section editors, it is comprised of articles written by leading experts in the field, providing a full review of the current status of each topic. The articles are up-to-date and fully illustrated with in-text references that allow readers to easily access primary literature. While all entries are authoritative and valuable to those with advanced understanding of evolutionary biology, they are also intended to be accessible to both advanced undergraduate and graduate students. Broad topics include the history of evolutionary biology, population genetics, quantitative genetics; speciation, life history evolution, evolution of sex and mating systems, evolutionary biogeography, evolutionary developmental biology, molecular and genome evolution, coevolution, phylogenetic methods, microbial evolution, diversification of plants and fungi, diversification of animals, and applied evolution. Presents fully comprehensive content, allowing easy access to fundamental information and links to primary research Contains concise articles by leading experts in the field that ensures current coverage of each topic Provides ancillary learning tools like tables, illustrations, and multimedia features to assist with the comprehension process
NbClust: an R package for determining the relevant number of clusters in a data set. ... APE: analyses of phylogenetics and evolution in r language.
Author: Jesús L. Romalde
Publisher: Frontiers Media SA
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.
HANDLING PHYLOGENIES IN R Almost all of the various metrics, analyses and graphical ... and statistical methods in ecological and evolutionary analyses.
Author: Marc W. Cadotte
Publisher: Princeton University Press
Phylogenies in Ecology is the first book to critically review the application of phylogenetic methods in ecology, and it serves as a primer to working ecologists and students of ecology wishing to understand these methods. This book demonstrates how phylogenetic information is transforming ecology by offering fresh ways to estimate the similarities and differences among species, and by providing deeper, evolutionary-based insights on species distributions, coexistence, and niche partitioning. Marc Cadotte and Jonathan Davies examine this emerging area's explosive growth, allowing for this new body of hypotheses testing. Cadotte and Davies systematically look at all the main areas of current ecophylogenetic methodology, testing, and inference. Each chapter of their book covers a unique topic, emphasizes key assumptions, and introduces the appropriate statistical methods and null models required for testing phylogenetically informed hypotheses. The applications presented throughout are supported and connected by examples relying on real-world data that have been analyzed using the open-source programming language, R. Showing how phylogenetic methods are shedding light on fundamental ecological questions related to species coexistence, conservation, and global change, Phylogenies in Ecology will interest anyone who thinks that evolution might be important in their data.
The caper package: comparative analysis of phylogenetics and evolution in R. Available online at: http://cran.r-project.org/web/packages/ ...
Author: Michelle L. Hall
Publisher: Frontiers Media SA
Category: Electronic book
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.