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Bayesian Evolutionary Analysis with BEAST

Bayesian Evolutionary Analysis with BEAST Author Alexei J. Drummond
ISBN-10 9781107019652
Release 2015-08-06
Pages 260
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Covers theory, practice and programming in Bayesian phylogenetics with BEAST. The why, how and what of BEAST 2.



Bayesian Evolutionary Analysis with BEAST

Bayesian Evolutionary Analysis with BEAST Author Alexei J. Drummond
ISBN-10 9781316298343
Release 2015-08-06
Pages
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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.



Analysis of Phylogenetics and Evolution with R

Analysis of Phylogenetics and Evolution with R Author Emmanuel Paradis
ISBN-10 9781461417439
Release 2011-11-06
Pages 386
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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.



Computational Molecular Evolution

Computational Molecular Evolution Author Ziheng Yang
ISBN-10 9780198566991
Release 2006-10-05
Pages 357
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This book describes the models, methods and algorithms that are most useful for analysing the ever-increasing supply of molecular sequence data, with a view to furthering our understanding of the evolution of genes and genomes.



Phylogenetics

Phylogenetics Author E. O. Wiley
ISBN-10 9781118017876
Release 2011-10-11
Pages 424
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The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology.



The Origins of Genome Architecture

The Origins of Genome Architecture Author Michael Lynch
ISBN-10 UOM:49015003406510
Release 2007
Pages 494
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The availability of genomic blueprints for hundreds of species has led to a transformation in biology, encouraging the proliferation of adaptive arguments for the evolution of genomic features, yet often sacrificing simpler, more compelling explanations. This textbook explains why the details matter and presents an explanatory framework for how the architectural diversity of eukarotic genomes and genes came to arise. Presented in non-technical fashion, it is compatible for use in an advanced Genetics course and as a professional reference.



Inferring Phylogenies

Inferring Phylogenies Author Joseph Felsenstein
ISBN-10 0878931775
Release 2004-01
Pages 664
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Phylogenies, or evolutionary trees, are the basic structures necessary to think about and analyze differences between species. Statistical, computational, and algorithmic work in this field has been ongoing for four decades now, and there have been great advances in understanding. Yet no book has summarized this work. Inferring Phylogenies does just that in a single, compact volume. Phylogenies are inferred with various kinds of data. This book concentrates on some of the central ones: discretely coded characters, molecular sequences, gene frequencies, and quantitative traits. Also covered are restriction sites, RAPDs, and microsatellites.



Evolutionary Pathways in Nature

Evolutionary Pathways in Nature Author John C. Avise
ISBN-10 9781139455039
Release 2006-05-04
Pages
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Reconstructing phylogenetic trees from DNA sequences has become a popular exercise in many branches of biology, and here the well-known geneticist John Avise explains why. Molecular phylogenies provide a genealogical backdrop for interpreting the evolutionary histories of many other types of biological traits (anatomical, behavioral, ecological, physiological, biochemical and even geographical). Guiding readers on a natural history tour along dozens of evolutionary pathways, the author describes how creatures ranging from microbes to elephants came to possess their current phenotypes. Essential reading for college students, professional biologists and anyone interested in natural history and biodiversity, this book is packed with fascinating examples of evolutionary puzzles from across the animal kingdom; how the toucan got its enormous bill, how reptiles grow back lost limbs and why Arctic fish don't freeze.



Tree Thinking

Tree Thinking Author David A. Baum
ISBN-10 1936221160
Release 2013
Pages 476
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Baum and Smith, both professors evolutionary biology and researchers in the field of systematics, present this highly accessible introduction to phylogenetics and its importance in modern biology. Ever since Darwin, the evolutionary histories of organisms have been portrayed in the form of branching trees or "phylogenies." However, the broad significance of the phylogenetic trees has come to be appreciated only quite recently. Phylogenetics has myriad applications in biology, from discovering the features present in ancestral organisms, to finding the sources of invasive species and infectious diseases, to identifying our closest living (and extinct) hominid relatives. Taking a conceptual approach, Tree Thinking introduces readers to the interpretation of phylogenetic trees, how these trees can be reconstructed, and how they can be used to answer biological questions. Examples and vivid metaphors are incorporated throughout, and each chapter concludes with a set of problems, valuable for both students and teachers. Tree Thinking is must-have textbook for any student seeking a solid foundation in this fundamental area of evolutionary biology.



Molecular Evolution

Molecular Evolution Author Ziheng Yang
ISBN-10 9780199602605
Release 2014
Pages 492
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"Studies of evolution at the molecular level have experienced phenomenal growth in the last few decades, due to rapid accumulation of genetic sequence data, improved computer hardware and software, and the development of sophisticated analytical methods. The flood of genomic data has generated an acute need for powerful statistical methods and efficient computational algorithms to enable their effective analysis and interpretation. This advanced textbook is aimed at graduate level students and professional researchers (both empiricists and theoreticians) in the fields of bioinformatics and computational biology, statistical genomics, evolutionary biology, molecular systematics, and population genetics. It will also be of relevance and use to a wider audience of applied statisticians, mathematicians, and computer scientists working in computational biology."--back cover.



Phylogenetic Networks

Phylogenetic Networks Author Daniel H. Huson
ISBN-10 9781139492874
Release 2010-12-02
Pages
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The evolutionary history of species is traditionally represented using a rooted phylogenetic tree. However, when reticulate events such as hybridization, horizontal gene transfer or recombination are believed to be involved, phylogenetic networks that can accommodate non-treelike evolution have an important role to play. This book provides the first interdisciplinary overview of phylogenetic networks. Beginning with a concise introduction to both phylogenetic trees and phylogenetic networks, the fundamental concepts and results are then presented for both rooted and unrooted phylogenetic networks. Current approaches and algorithms available for computing phylogenetic networks from different types of datasets are then discussed, accompanied by examples of their application to real biological datasets. The book also summarises the algorithms used for drawing phylogenetic networks, along with the existing software for their computation and evaluation. All datasets, examples and other additional information and links are available from the book's companion website at www.phylogenetic-networks.org.



Beast

Beast Author Brie Spangler
ISBN-10 9781101937167
Release 2016
Pages 336
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After falling off the roof, fifteen-year-old misfit Dylan must attend a therapy group for self-harmers where he meets Jamie, a beautiful and amazing person he doesn't know is transgender.



Bayesian Phylogenetics

Bayesian Phylogenetics Author Ming-Hui Chen
ISBN-10 9781466500792
Release 2014-05-27
Pages 396
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Offering a rich diversity of models, Bayesian phylogenetics allows evolutionary biologists, systematists, ecologists, and epidemiologists to obtain answers to very detailed phylogenetic questions. Suitable for graduate-level researchers in statistics and biology, Bayesian Phylogenetics: Methods, Algorithms, and Applications presents a snapshot of current trends in Bayesian phylogenetic research. Encouraging interdisciplinary research, this book introduces state-of-the-art phylogenetics to the Bayesian statistical community and, likewise, presents state-of-the-art Bayesian statistics to the phylogenetics community. The book emphasizes model selection, reflecting recent interest in accurately estimating marginal likelihoods. It also discusses new approaches to improve mixing in Bayesian phylogenetic analyses in which the tree topology varies. In addition, the book covers divergence time estimation, biologically realistic models, and the burgeoning interface between phylogenetics and population genetics.



The Phylogenetic Handbook

The Phylogenetic Handbook Author Philippe Lemey
ISBN-10 1139478613
Release 2009-03-26
Pages
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The Phylogenetic Handbook is a broad, hands on guide to theory and practice of nucleotide and protein phylogenetic analysis. This second edition includes six new chapters, covering topics such as Bayesian inference, tree topology testing and the impact of recombination on phylogenies, as well as a detailed section on molecular adaptation. The book has a stronger focus on hypothesis testing than the previous edition, with more extensive discussions on recombination analysis, detecting molecular adaptation and genealogy-based population genetics. Many chapters include elaborate practical sections, which have been updated to introduce the reader to the most recent versions of sequence analysis and phylogeny software, including BLAST, FastA, Clustal, T-coffee, Muscle, DAMBE, Tree-puzzle, Phylip, MEGA, PAUP*, IQPNNI, CONSEL, ModelTest, Prottest, PAML, HYPHY, MrBayes, BEAST, LAMARC, SplitsTree, and RDP. Many analysis tools are described by their original authors, resulting in clear explanations that constitute an ideal teaching guide for advanced-level undergraduate and graduate students.



Phylogenetic Trees Made Easy

Phylogenetic Trees Made Easy Author Barry G. Hall
ISBN-10 0878936068
Release 2011
Pages 282
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Barry G. Hall helps beginners get started in creating phylogenetic trees from protein or nucleic acid sequence data.



The Phylogenetic Handbook

The Phylogenetic Handbook Author Marco Salemi
ISBN-10 052180390X
Release 2003-08-27
Pages 406
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Introduction to the theory and practice of phylogenetic analysis for molecular evolution students and professionals.



Crime Genes Neuroscience and Cyberspace

Crime  Genes  Neuroscience and Cyberspace Author Tim Owen
ISBN-10 9781137526885
Release 2017-09-18
Pages 232
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This book applies Owen’s unique genetic-social framework to the study of crime and criminal behaviour, with an emphasis on cybercrime. Moving beyond challenges which confront contemporary criminological theorizing such as: the stagnation of critical criminology, the relativistic nihilism of the ‘cultural turn’, posthumanism, and virtual criminology, the author codifies and ‘applies’ the latest version of the framework to the study of crime, both in and out of cyberspace. Drawing upon evolutionary psychology, behavioural genetics and the philosophy of Heidegger, he introduces new terms such as ‘Neuro-Agency’ and notions of Embodied Cognition into criminological theorizing. Adopting a soft compatibilist approach to free-will, and Realist ontology, Owen’s meta-theoretical focus provides a new direction for criminological theorizing, in particular in the direction of the conceptualization and prediction of cyber violence. Exciting and timely, this book will appeal to scholars and advanced students of criminology, law, sociology, social policy, psychology, philosophy, policing and forensic investigation.