Bayesian Phylogenetics

by Ming-Hui Chen
Bayesian Phylogenetics
Author: Ming-Hui Chen
Publisher: CRC Press
Total Pages: 398
Release: 2014-05-27
Genre: Mathematics
ISBN: 1466500794
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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.

Bayesian Phylogenetics

by Ming-Hui Chen
Bayesian Phylogenetics
Author: Ming-Hui Chen
Publisher: CRC Press
Total Pages: 396
Release: 2014-05-27
Genre: Mathematics
ISBN: 1466500824
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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 c

Bayesian Evolutionary Analysis with BEAST

by Alexei J. Drummond
Bayesian Evolutionary Analysis with BEAST
Author: Alexei J. Drummond
Publisher: Cambridge University Press
Total Pages: 263
Release: 2015-08-06
Genre: Science
ISBN: 1316298345
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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

by Emmanuel Paradis
Analysis of Phylogenetics and Evolution with R
Author: Emmanuel Paradis
Publisher: Springer Science & Business Media
Total Pages: 221
Release: 2006-11-25
Genre: Science
ISBN: 0387351000
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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.

The Phylogenetic Handbook

by Marco Salemi
The Phylogenetic Handbook
Author: Marco Salemi
Publisher: Cambridge University Press
Total Pages: 750
Release: 2009-03-26
Genre: Science
ISBN: 0521877105
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A broad, hands on guide with detailed explanations of current methodology, relevant exercises and popular software tools.

Phylogenetics

by E. O. Wiley
Phylogenetics
Author: E. O. Wiley
Publisher: John Wiley & Sons
Total Pages: 444
Release: 2011-10-11
Genre: Science
ISBN: 1118017870
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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.

Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology

by László Zsolt Garamszegi
Modern Phylogenetic Comparative Methods and Their Application in Evolutionary Biology
Author: László Zsolt Garamszegi
Publisher: Springer
Total Pages: 553
Release: 2014-07-29
Genre: Science
ISBN: 3662435500
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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.

The Handbook of Historical Linguistics, Volume II

by Richard D. Janda
The Handbook of Historical Linguistics, Volume II
Author: Richard D. Janda
Publisher: John Wiley & Sons
Total Pages: 640
Release: 2020-09-15
Genre: Language Arts & Disciplines
ISBN: 111873226X
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An entirely new follow-up volume providing a detailed account of numerous additional issues, methods, and results that characterize current work in historical linguistics. This brand-new, second volume of The Handbook of Historical Linguistics is a complement to the well-established first volume first published in 2003. It includes extended content allowing uniquely comprehensive coverage of the study of language(s) over time. Though it adds fresh perspectives on several topics previously treated in the first volume, this Handbook focuses on extensions of diachronic linguistics beyond those key issues. This Handbook provides readers with studies of language change whose perspectives range from comparisons of large open vs. small closed corpora, via creolistics and linguistic contact in general, to obsolescence and endangerment of languages. Written by leading scholars in their respective fields, new chapters are offered on matters such as the origin of language, evidence from language for reconstructing human prehistory, invocations of language present in studies of language past, benefits of linguistic fieldwork for historical investigation, ways in which not only biological evolution but also field biology can serve as heuristics for research into the rise and spread of linguistic innovations, and more. Moreover, it: offers novel and broadened content complementing the earlier volume so as to provide the fullest available overview of a wholly engrossing field includes 23 all-new contributed chapters, treating some familiar themes from fresh perspectives but mostly covering entirely new topics features expanded discussion of material from language families other than Indo-European provides a multiplicity of views from numerous specialists in linguistic diachrony. The Handbook of Historical Linguistics, Volume II is an ideal book for undergraduate and graduate students in linguistics, researchers and professional linguists, as well as all those interested in the history of particular languages and the history of language more generally.

Molecular Evolution

by Ziheng Yang
Molecular Evolution
Author: Ziheng Yang
Publisher: Oxford University Press
Total Pages: 509
Release: 2014
Genre: Science
ISBN: 0199602603
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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. Molecular Evolution: a statistical approach presents and explains modern statistical methods and computational algorithms for the comparative analysis of genetic sequence data in the fields of molecular evolution, molecular phylogenetics, statistical phylogeography, and comparative genomics. Written by an expert in the field, the book emphasizes conceptual understanding rather than mathematical proofs. The text is enlivened with numerous examples of real data analysis and numerical calculations to illustrate the theory, in addition to the working problems at the end of each chapter. The coverage of maximum likelihood and Bayesian methods are in particular up-to-date, comprehensive, and authoritative. 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.