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Estimating Species Trees

Author: L. Lacey Knowles
Publisher: John Wiley & Sons
ISBN: 1118211405
Size: 35.23 MB
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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.

Phylogenomics

Author: Christoph Bleidorn
Publisher: Springer
ISBN: 3319540645
Size: 34.37 MB
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This unique textbook provides a clear and concise overview of the key principles of the complex field of phylogenomics, with a particular focus on sequencing technologies that are crucial to studying and understanding interrelations in evolutionary genomics. It includes chapters dedicated to the analysis of nucleotide sequences using assembling and alignment methods and also discusses the main strategies for phylogenetic studies, systematic errors and their correction. This highly readable textbook is intended for graduate students and young researchers with an interest in phylogenetics and evolutionary developmental biology.

Object Lessons And The Formation Of Knowledge

Author: Kerstin Barndt
Publisher: University of Michigan Press
ISBN: 0472122649
Size: 70.51 MB
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Object Lessons and the Formation of Knowledge explores the museums, libraries, and special collections of the University of Michigan on its bicentennial. Since its inception, U-M has collected and preserved objects: biological and geological specimens; ethnographic and archaeological artifacts; photographs and artistic works; encyclopedia, textbooks, rare books, and documents; and many other items. These vast collections and libraries testify to an ambitious vision of the research university as a place where knowledge is accumulated, shared, and disseminated through teaching, exhibition, and publication. Today, two hundred years after the university’s founding, museums, libraries, and archives continue to be an important part of U-M, which maintains more than twenty distinct museums, libraries, and collections. Viewed from a historic perspective, they provide a window through which we can explore the transformation of the academy, its public role, and the development of scholarly disciplines over the last two centuries. Even as they speak to important facets of Michigan’s history, many of these collections also remain essential to academic research, knowledge production, and object-based pedagogy. Moreover, the university’s exhibitions and displays attract hundreds of thousands of visitors per year from the campus, regional, and global communities. Beautifully illustrated with color photographs of these world-renowned collections, this book will appeal to readers interested in the history of museums and collections, the formation of academic disciplines, and of course the University of Michigan.

Bayesian Evolutionary Analysis With Beast

Author: Alexei J. Drummond
Publisher: Cambridge University Press
ISBN: 1316298345
Size: 27.48 MB
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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.

Molecular Evolution

Author: Roderick D.M. Page
Publisher: John Wiley & Sons
ISBN: 1444313363
Size: 80.32 MB
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The study of evolution at the molecular level has given the subject of evolutionary biology a new significance. Phylogenetic 'trees' of gene sequences are a powerful tool for recovering evolutionary relationships among species, and can be used to answer a broad range of evolutionary and ecological questions. They are also beginning to permeate the medical sciences. In this book, the authors approach the study of molecular evolution with the phylogenetic tree as a central metaphor. This will equip students and professionals with the ability to see both the evolutionary relevance of molecular data, and the significance evolutionary theory has for molecular studies. The book is accessible yet sufficiently detailed and explicit so that the student can learn the mechanics of the procedures discussed. The book is intended for senior undergraduate and graduate students taking courses in molecular evolution/phylogenetic reconstruction. It will also be a useful supplement for students taking wider courses in evolution, as well as a valuable resource for professionals. First student textbook of phylogenetic reconstruction which uses the tree as a central metaphor of evolution. Chapter summaries and annotated suggestions for further reading. Worked examples facilitate understanding of some of the more complex issues. Emphasis on clarity and accessibility.

The Theory Of Island Biogeography

Author: Robert H. MacArthur
Publisher: Princeton University Press
ISBN: 1400881374
Size: 57.52 MB
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Biogeography was stuck in a "natural history phase" dominated by the collection of data, the young Princeton biologists Robert H. MacArthur and Edward O. Wilson argued in 1967. In this book, the authors developed a general theory to explain the facts of island biogeography. The theory builds on the first principles of population ecology and genetics to explain how distance and area combine to regulate the balance between immigration and extinction in island populations. The authors then test the theory against data. The Theory of Island Biogeography was never intended as the last word on the subject. Instead, MacArthur and Wilson sought to stimulate new forms of theoretical and empirical studies, which will lead in turn to a stronger general theory. Even a third of a century since its publication, the book continues to serve that purpose well. From popular books like David Quammen's Song of the Dodo to arguments in the professional literature, The Theory of Island Biogeography remains at the center of discussions about the geographic distribution of species. In a new preface, Edward O. Wilson reviews the origins and consequences of this classic book.

Molecular Phylogeny Of Microorganisms

Author: Aharon Oren
Publisher: Horizon Scientific Press
ISBN: 1904455670
Size: 78.13 MB
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An introduction to molecular phylogeny, this text provides an overview of the diversity, systematics and nomenclature of microbes in many branches of biological science.

Understanding Machine Learning

Author: Shai Shalev-Shwartz
Publisher: Cambridge University Press
ISBN: 1107057132
Size: 72.66 MB
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Introduces machine learning and its algorithmic paradigms, explaining the principles behind automated learning approaches and the considerations underlying their usage.

Biodiversity

Author: David L. Hawksworth
Publisher: Springer Science & Business Media
ISBN: 9780412752209
Size: 63.12 MB
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Leading experts on the field of biodiversity examine examples from a wide range of organism groups. Their approaches include the latest molecular and phylogenetic techniques through to the selection of indicator data and aspects of sampling. This paperback edition has been published for students on 'biodiversity' related courses.

Reasoning About Knowledge

Author: Ronald Fagin
Publisher: MIT Press
ISBN: 9780262562003
Size: 12.18 MB
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Reasoning about knowledge—particularly the knowledge of agents who reason about the world and each other's knowledge—was once the exclusive province of philosophers and puzzle solvers. More recently, this type of reasoning has been shown to play a key role in a surprising number of contexts, from understanding conversations to the analysis of distributed computer algorithms. Reasoning About Knowledge is the first book to provide a general discussion of approaches to reasoning about knowledge and its applications to distributed systems, artificial intelligence, and game theory. It brings eight years of work by the authors into a cohesive framework for understanding and analyzing reasoning about knowledge that is intuitive, mathematically well founded, useful in practice, and widely applicable. The book is almost completely self-contained and should be accessible to readers in a variety of disciplines, including computer science, artificial intelligence, linguistics, philosophy, cognitive science, and game theory. Each chapter includes exercises and bibliographic notes.