ANALYSIS OF PHYLOGENETICS AND EVOLUTION WITH R

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Analysis Of Phylogenetics And Evolution With R

Author : Emmanuel Paradis
ISBN : 9781461417439
Genre : Science
File Size : 69.36 MB
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The increasing availability of molecular and genetic databases coupled with the growing power of computers gives biologists opportunities to address new issues, such as the patterns of molecular evolution, and re-assess old ones, such as the role of adaptation in species diversification. In the second edition, the book continues to integrate a wide variety of data analysis methods into a single and flexible interface: the R language. This open source language is available for a wide range of computer systems and has been adopted as a computational environment by many authors of statistical software. Adopting R as a main tool for phylogenetic analyses will ease the workflow in biologists' data analyses, ensure greater scientific repeatability, and enhance the exchange of ideas and methodological developments. The second edition is completed updated, covering the full gamut of R packages for this area that have been introduced to the market since its previous publication five years ago. There is also a new chapter on the simulation of evolutionary data. Graduate students and researchers in evolutionary biology can use this book as a reference for data analyses, whereas researchers in bioinformatics interested in evolutionary analyses will learn how to implement these methods in R. The book starts with a presentation of different R packages and gives a short introduction to R for phylogeneticists unfamiliar with this language. The basic phylogenetic topics are covered: manipulation of phylogenetic data, phylogeny estimation, tree drawing, phylogenetic comparative methods, and estimation of ancestral characters. The chapter on tree drawing uses R's powerful graphical environment. A section deals with the analysis of diversification with phylogenies, one of the author's favorite research topics. The last chapter is devoted to the development of phylogenetic methods with R and interfaces with other languages (C and C++). Some exercises conclude these chapters.
Category: Science

Ecological Statistics

Author : Gordon A. Fox
ISBN : 9780191652882
Genre : Science
File Size : 54.14 MB
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The application and interpretation of statistics are central to ecological study and practice. Ecologists are now asking more sophisticated questions than in the past. These new questions, together with the continued growth of computing power and the availability of new software, have created a new generation of statistical techniques. These have resulted in major recent developments in both our understanding and practice of ecological statistics. This novel book synthesizes a number of these changes, addressing key approaches and issues that tend to be overlooked in other books such as missing/censored data, correlation structure of data, heterogeneous data, and complex causal relationships. These issues characterize a large proportion of ecological data, but most ecologists' training in traditional statistics simply does not provide them with adequate preparation to handle the associated challenges. Uniquely, Ecological Statistics highlights the underlying links among many statistical approaches that attempt to tackle these issues. In particular, it gives readers an introduction to approaches to inference, likelihoods, generalized linear (mixed) models, spatially or phylogenetically-structured data, and data synthesis, with a strong emphasis on conceptual understanding and subsequent application to data analysis. Written by a team of practicing ecologists, mathematical explanations have been kept to the minimum necessary. This user-friendly textbook will be suitable for graduate students, researchers, and practitioners in the fields of ecology, evolution, environmental studies, and computational biology who are interested in updating their statistical tool kits. A companion web site provides example data sets and commented code in the R language.
Category: Science

Methods In Comparative Plant Population Ecology

Author : David Gibson
ISBN : 9780199671472
Genre : Science
File Size : 69.68 MB
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This second edition provides authoritative guidance on research methodology for plant population ecology. Practical advice is provided to assist senior undergraduates and post-graduate students, and all researchers, design their own field and greenhouse experiments and establish a research programme in plant population ecology.
Category: Science

Scales And Hierarchies

Author : Ina Bornkessel-Schlesewsky
ISBN : 9783110395006
Genre : Language Arts & Disciplines
File Size : 32.29 MB
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The volume advances our understanding of the role of scales and hierarchies across the linguistic sciences. Although scales and hierarchies are widely assumed to play a role in the modelling of linguistic phenomena, their status remains controversial, and it is these controversies that the present volume tackles head-on.
Category: Language Arts & Disciplines

Metabolic Ecology

Author : Richard M. Sibly
ISBN : 9781119968511
Genre : Science
File Size : 65.19 MB
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One of the first textbooks in this emerging important field of ecology. Most of ecology is about metabolism: the ways that organisms use energy and materials. The energy requirements of individuals – their metabolic rates – vary predictably with their body size and temperature. Ecological interactions are exchanges of energy and materials between organisms and their environments. So metabolic rate affects ecological processes at all levels: individuals, populations, communities and ecosystems. Each chapter focuses on a different process, level of organization, or kind of organism. It lays a conceptual foundation and presents empirical examples. Together, the chapters provide an integrated framework that holds the promise for a unified theory of ecology. The book is intended to be accessible to upper-level undergraduate, and graduate students, but also of interest to senior scientists. Its easy-to-read chapters and clear illustrations can be used in lecture and seminar courses. Together they make for an authoritative treatment that will inspire future generations to study metabolic ecology.
Category: Science

Austral Hepaticae

Author : Rudolf Mathias Schuster
ISBN : UCSD:31822009211467
Genre : Liverworts
File Size : 20.94 MB
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The proliferation of "species" -- often placed in the "wrong" genus, has impacted all taxonamic work in 20th Century hepaticology. The same species may have been described under 3-4, or more, genera; under a single genus, such as Lepidolejeunea, species have been described in some 10-12 genera. The author has conducted field work in the Antipodes for over 40 years, starting in Fuegia in 1960. He has not only become familiar with all the chief groups as living plants, but has studied them microscopically in areas as diverse as Fiji, the Prince Edward Islands., Campbell I., Chile and New Zealand, residing for months or sometimes years in these regions. The opportunity to study hepatics in the field has given him a unique opportunity to learn these organisms as living entities; to drawt cytological details from living plants, and to place critical material into FAA for subsequent illustration, especially of the ephemeral sporophytes. Unlike most extant taxonamic works, which are based on herbarium study, this work tries to give the reader a "feeling" for the many taxa as living organisms.
Category: Liverworts

Molecular Evolution And Phylogenetics

Author : Masatoshi Nei
ISBN : 0195350510
Genre : Science
File Size : 72.45 MB
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During the last ten years, remarkable progress has occurred in the study of molecular evolution. Among the most important factors that are responsible for this progress are the development of new statistical methods and advances in computational technology. In particular, phylogenetic analysis of DNA or protein sequences has become a powerful tool for studying molecular evolution. Along with this developing technology, the application of the new statistical and computational methods has become more complicated and there is no comprehensive volume that treats these methods in depth. Molecular Evolution and Phylogenetics fills this gap and present various statistical methods that are easily accessible to general biologists as well as biochemists, bioinformatists and graduate students. The text covers measurement of sequence divergence, construction of phylogenetic trees, statistical tests for detection of positive Darwinian selection, inference of ancestral amino acid sequences, construction of linearized trees, and analysis of allele frequency data. Emphasis is given to practical methods of data analysis, and methods can be learned by working through numerical examples using the computer program MEGA2 that is provided.
Category: Science

Molecular Evolution Producing The Biochemical Data

Author :
ISBN : 9780080455150
Genre : Science
File Size : 41.66 MB
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The critically acclaimed laboratory standard, Methods in Enzymology, is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. The series contains much material still relevant today - truly an essential publication for researchers in all fields of life sciences. Molecular Evolution Producing the Biochemical Data part B is a continuation of methods published in Part A (1993, volume 224). The work is a very methodological look at markers, templates, genomes, datasets and analyses used in studies of biological diversity. * One of the most highly respected publications in the field of biochemistry since 1955 * Frequently consulted, and praised by researchers and reviewers alike * Truly an essential publication for anyone in any field of the life sciences
Category: Science

Bayesian Evolutionary Analysis With Beast

Author : Alexei J. Drummond
ISBN : 9781107019652
Genre : Science
File Size : 49.79 MB
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Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.
Category: Science