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Inferring Large Phylogenies
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Book Synopsis Inferring Phylogenies by : Joseph Felsenstein
Download or read book Inferring Phylogenies written by Joseph Felsenstein and published by Sinauer Associates Incorporated. This book was released on 2004-01 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Statistics and Truth by : Calyampudi Radhakrishna Rao
Download or read book Statistics and Truth written by Calyampudi Radhakrishna Rao and published by World Scientific. This book was released on 1997 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by one of the top most statisticians with experience in diverse fields of applications of statistics, the book deals with the philosophical and methodological aspects of information technology, collection and analysis of data to provide insight into a problem, whether it is scientific research, policy making by government or decision making in our daily lives.The author dispels the doubts that chance is an expression of our ignorance which makes accurate prediction impossible and illustrates how our thinking has changed with quantification of uncertainty by showing that chance is no longer the obstructor but a way of expressing our knowledge. Indeed, chance can create and help in the investigation of truth. It is eloquently demonstrated with numerous examples of applications that statistics is the science, technology and art of extracting information from data and is based on a study of the laws of chance. It is highlighted how statistical ideas played a vital role in scientific and other investigations even before statistics was recognized as a separate discipline and how statistics is now evolving as a versatile, powerful and inevitable tool in diverse fields of human endeavor such as literature, legal matters, industry, archaeology and medicine.Use of statistics to the layman in improving the quality of life through wise decision making is emphasized.
Book Synopsis Phylogenetic Networks by : Daniel H. Huson
Download or read book Phylogenetic Networks written by Daniel H. Huson and published by Cambridge University Press. This book was released on 2010-12-02 with total page 376 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Bioinformatics and Phylogenetics by : Tandy Warnow
Download or read book Bioinformatics and Phylogenetics written by Tandy Warnow and published by Springer. This book was released on 2019-04-08 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a compelling collection of state-of-the-art work in algorithmic computational biology, honoring the legacy of Professor Bernard M.E. Moret in this field. Reflecting the wide-ranging influences of Prof. Moret’s research, the coverage encompasses such areas as phylogenetic tree and network estimation, genome rearrangements, cancer phylogeny, species trees, divide-and-conquer strategies, and integer linear programming. Each self-contained chapter provides an introduction to a cutting-edge problem of particular computational and mathematical interest. Topics and features: addresses the challenges in developing accurate and efficient software for the NP-hard maximum likelihood phylogeny estimation problem; describes the inference of species trees, covering strategies to scale phylogeny estimation methods to large datasets, and the construction of taxonomic supertrees; discusses the inference of ultrametric distances from additive distance matrices, and the inference of ancestral genomes under genome rearrangement events; reviews different techniques for inferring evolutionary histories in cancer, from the use of chromosomal rearrangements to tumor phylogenetics approaches; examines problems in phylogenetic networks, including questions relating to discrete mathematics, and issues of statistical estimation; highlights how evolution can provide a framework within which to understand comparative and functional genomics; provides an introduction to Integer Linear Programming and its use in computational biology, including its use for solving the Traveling Salesman Problem. Offering an invaluable source of insights for computer scientists, applied mathematicians, and statisticians, this illuminating volume will also prove useful for graduate courses on computational biology and bioinformatics.
Book Synopsis Information-theoretic causal inference of lexical flow by : Johannes Dellert
Download or read book Information-theoretic causal inference of lexical flow written by Johannes Dellert and published by Language Science Press. This book was released on 2019 with total page 385 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume seeks to infer large phylogenetic networks from phonetically encoded lexical data and contribute in this way to the historical study of language varieties. The technical step that enables progress in this case is the use of causal inference algorithms. Sample sets of words from language varieties are preprocessed into automatically inferred cognate sets, and then modeled as information-theoretic variables based on an intuitive measure of cognate overlap. Causal inference is then applied to these variables in order to determine the existence and direction of influence among the varieties. The directed arcs in the resulting graph structures can be interpreted as reflecting the existence and directionality of lexical flow, a unified model which subsumes inheritance and borrowing as the two main ways of transmission that shape the basic lexicon of languages. A flow-based separation criterion and domain-specific directionality detection criteria are developed to make existing causal inference algorithms more robust against imperfect cognacy data, giving rise to two new algorithms. The Phylogenetic Lexical Flow Inference (PLFI) algorithm requires lexical features of proto-languages to be reconstructed in advance, but yields fully general phylogenetic networks, whereas the more complex Contact Lexical Flow Inference (CLFI) algorithm treats proto-languages as hidden common causes, and only returns hypotheses of historical contact situations between attested languages. The algorithms are evaluated both against a large lexical database of Northern Eurasia spanning many language families, and against simulated data generated by a new model of language contact that builds on the opening and closing of directional contact channels as primary evolutionary events. The algorithms are found to infer the existence of contacts very reliably, whereas the inference of directionality remains difficult. This currently limits the new algorithms to a role as exploratory tools for quickly detecting salient patterns in large lexical datasets, but it should soon be possible for the framework to be enhanced e.g. by confidence values for each directionality decision.
Book Synopsis Molecular Evolution and Phylogenetics by : Masatoshi Nei
Download or read book Molecular Evolution and Phylogenetics written by Masatoshi Nei and published by Oxford University Press. This book was released on 2000-07-27 with total page 444 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Evolution by : Roderick D.M. Page
Download or read book Molecular Evolution written by Roderick D.M. Page and published by John Wiley & Sons. This book was released on 2009-07-14 with total page 352 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis The Evolution of Population Biology by : Rama S. Singh
Download or read book The Evolution of Population Biology written by Rama S. Singh and published by Cambridge University Press. This book was released on 2004-01-15 with total page 492 pages. Available in PDF, EPUB and Kindle. Book excerpt: This 2004 collection of essays deals with the foundation and historical development of population biology and its relationship to population genetics and population ecology on the one hand and to the rapidly growing fields of molecular quantitative genetics, genomics and bioinformatics on the other. Such an interdisciplinary treatment of population biology has never been attempted before. The volume is set in a historical context, but it has an up-to-date coverage of material in various related fields. The areas covered are the foundation of population biology, life history evolution and demography, density and frequency dependent selection, recent advances in quantitative genetics and bioinformatics, evolutionary case history of model organisms focusing on polymorphisms and selection, mating system evolution and evolution in the hybrid zones, and applied population biology including conservation, infectious diseases and human diversity. This is the third of three volumes published in honour of Richard Lewontin.
Book Synopsis Early Events in Monocot Evolution by : Paul Wilkin
Download or read book Early Events in Monocot Evolution written by Paul Wilkin and published by Cambridge University Press. This book was released on 2013-05-30 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: Tracing the evolution of one of the most ancient major branches of flowering plants, this is a wide-ranging survey of state-of-the-art research on the early clades of the monocot phylogenetic tree. It explores a series of broad but linked themes, providing for the first time a detailed and coherent view of the taxa of the early monocot lineages, how they diversified and their importance in monocots as a whole. Featuring contributions from leaders in the field, the chapters trace the evolution of the monocots from largely aquatic ancestors. Topics covered include the rapidly advancing field of monocot fossils, aquatic adaptations in pollen and anther structure and pollination strategies and floral developmental morphology. The book also presents a new plastid sequence analysis of early monocots and a review of monocot phylogeny as a whole, placing in an evolutionary context a plant group of major ecological, economic and horticultural importance.
Book Synopsis Analysis of Phylogenetics and Evolution with R by : Emmanuel Paradis
Download or read book Analysis of Phylogenetics and Evolution with R written by Emmanuel Paradis and published by Springer Science & Business Media. This book was released on 2006-11-25 with total page 221 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Evolutionary Genetics by : Charles W. Fox
Download or read book Evolutionary Genetics written by Charles W. Fox and published by Oxford University Press. This book was released on 2006-04-27 with total page 618 pages. Available in PDF, EPUB and Kindle. Book excerpt: Charles Fox and Jason Wolf have brought together leading researchers to produce a cutting-edge primer introducing readers to the major concepts in modern evolutionary genetics. This book spans the continuum of scale, from studies of DNA sequence evolution through proteins and development to multivariate phenotypic evolution, and the continuum of time, from ancient events that lead to current species diversity to the rapid evolution seen over relatively short time scales in experimental evolution studies. Chapters are accessible to an audience lacking extensive background in evolutionaryy genetics but also current and in-depth enough to be of value to established researchers in evolution biology.
Book Synopsis Phylogenetic Analysis of DNA Sequences by : Michael M. Miyamoto
Download or read book Phylogenetic Analysis of DNA Sequences written by Michael M. Miyamoto and published by Oxford University Press. This book was released on 1991-11-14 with total page 369 pages. Available in PDF, EPUB and Kindle. Book excerpt: With increasing frequency, systematic and evolutionary biologists have turned to the techniques of molecular biology to complement their traditional morphological and anatomical approaches to questions of the historical relationship and descent among groups of animals and plants. In particular, the comparative analysis of DNA sequences is becoming a common and important focus of research attention today. The objective of this volume is to survey the emerging field of molecular systematics of DNA sequences, and to appraise the strengths and limitations of the different approaches yielded by these techniques. The contributors are an internationally recognized group of investigators from different schools and disciplines who critically address a diversity of crucial questions about DNA systematics, including DNA sequence data acquisition, phylogenetic inference, congruence and consensus problems, limitations of molecular data, and the integration of molecular and morphological data sets. The work will interest all botanists and zoologists involved in systematics, taxonomy, and evolution.
Book Synopsis Algorithms in Bioinformatics by : Steven L. Salzberg
Download or read book Algorithms in Bioinformatics written by Steven L. Salzberg and published by Springer Science & Business Media. This book was released on 2009-08-28 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: These proceedings contain papers from the 2009 Workshop on Algorithms in Bioinformatics (WABI), held at the University of Pennsylvania in Philadelphia, Pennsylvania during September 12–13, 2009. WABI 2009 was the ninth annual conference in this series, which focuses on novel algorithms that address imp- tantproblemsingenomics,molecularbiology,andevolution.Theconference- phasizes research that describes computationally e?cient algorithms and data structures that have been implemented and tested in simulations and on real data. WABI is sponsored by the European Association for Theoretical C- puter Science (EATCS) and the International Society for Computational Bi- ogy (ISCB). WABI 2009 was supported by the Penn Genome Frontiers Institute and the Penn Center for Bioinformatics at the University of Pennsylvania. For the 2009 conference, 90 full papers were submitted for review by the Program Committee, and from this strong ?eld of submissions, 34 papers were chosen for presentation at the conference and publication in the proceedings. The ?nal programcovered a wide range of topics including gene interaction n- works, molecular phylogeny, RNA and protein structure, and genome evolution.
Book Synopsis Molecular Evolution by : Ziheng Yang
Download or read book Molecular Evolution written by Ziheng Yang and published by Oxford University Press. This book was released on 2014 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis 2010 Gateway Computing Environments Workshop by : IEEE Staff
Download or read book 2010 Gateway Computing Environments Workshop written by IEEE Staff and published by . This book was released on 2010-12 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Phylogenetic Ecology by : Nathan G. Swenson
Download or read book Phylogenetic Ecology written by Nathan G. Swenson and published by University of Chicago Press. This book was released on 2019-11-22 with total page 229 pages. Available in PDF, EPUB and Kindle. Book excerpt: Over the past decade, ecologists have increasingly embraced phylogenetics, the study of evolutionary relationships among species. As a result, they have come to discover the field’s power to illuminate present ecological patterns and processes. Ecologists are now investigating whether phylogenetic diversity is a better measure of ecosystem health than more traditional metrics like species diversity, whether it can predict the future structure and function of communities and ecosystems, and whether conservationists might prioritize it when formulating conservation plans. In Phylogenetic Ecology, Nathan G. Swenson synthesizes this nascent field’s major conceptual, methodological, and empirical developments to provide students and practicing ecologists with a foundational overview. Along the way, he highlights those realms of phylogenetic ecology that will likely increase in relevance—such as the burgeoning subfield of phylogenomics—and shows how ecologists might lean on these new perspectives to inform their research programs.
Book Synopsis Statistical Population Genomics by : Julien Y Dutheil
Download or read book Statistical Population Genomics written by Julien Y Dutheil and published by . This book was released on 2020-10-08 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access volume presents state-of-the-art inference methods in population genomics, focusing on data analysis based on rigorous statistical techniques. After introducing general concepts related to the biology of genomes and their evolution, the book covers state-of-the-art methods for the analysis of genomes in populations, including demography inference, population structure analysis and detection of selection, using both model-based inference and simulation procedures. Last but not least, it offers an overview of the current knowledge acquired by applying such methods to a large variety of eukaryotic organisms. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, pointers to the relevant literature, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Statistical Population Genomics aims to promote and ensure successful applications of population genomic methods to an increasing number of model systems and biological questions. This work was published by Saint Philip Street Press pursuant to a Creative Commons license permitting commercial use. All rights not granted by the work's license are retained by the author or authors.
