Search Results for a-mathematical-primer-of-molecular-phylogenetics

This volume, A Mathematical Primer of Molecular Phylogenetics, offers a unique perspective on a number of phylogenetic issues that have not been covered in detail in previous publications.

Author: Xuhua Xia

Publisher: CRC Press

ISBN: 9780429759307

Category: Science

Page: 366

View: 491

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This volume, A Mathematical Primer of Molecular Phylogenetics, offers a unique perspective on a number of phylogenetic issues that have not been covered in detail in previous publications. The volume provides sufficient mathematical background for young mathematicians and computational scientists, as well as mathematically inclined biology students, to make a smooth entry into the expanding field of molecular phylogenetics. The book will also provide sufficient details for researchers in phylogenetics to understand the workings of existing software packages used. The volume offers comprehensive but detailed numerical illustrations to render difficult mathematical and computational concepts in molecular phylogenetics accessible to a variety of readers with different academic background. The text includes examples of solved problems after each chapter, which will be particularly helpful for fourth-year undergraduates, postgraduates, and postdoctoral students in biology, mathematics and computer sciences. Researchers in molecular biology and evolution will find it very informative as well.
2020-04-13 By Xuhua Xia

Library and Archives Canada Cataloguing in Publication Title: A mathematical primer of molecular phylogenetics / Xuhua Xia. Names: Xia, Xuhua, 1959- author. Description: Includes bibliographical references and index.

Author: Xuhua Xia

Publisher: CRC Press

ISBN: 9780429759314

Category: Science

Page: 366

View: 491

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This volume, A Mathematical Primer of Molecular Phylogenetics, offers a unique perspective on a number of phylogenetic issues that have not been covered in detail in previous publications. The volume provides sufficient mathematical background for young mathematicians and computational scientists, as well as mathematically inclined biology students, to make a smooth entry into the expanding field of molecular phylogenetics. The book will also provide sufficient details for researchers in phylogenetics to understand the workings of existing software packages used. The volume offers comprehensive but detailed numerical illustrations to render difficult mathematical and computational concepts in molecular phylogenetics accessible to a variety of readers with different academic background. The text includes examples of solved problems after each chapter, which will be particularly helpful for fourth-year undergraduates, postgraduates, and postdoctoral students in biology, mathematics and computer sciences. Researchers in molecular biology and evolution will find it very informative as well.
2020-04-13 By Xuhua Xia

Table of contents

Author: Olivier Gascuel

Publisher: Oxford University Press on Demand

ISBN: 9780198566106

Category: Mathematics

Page: 416

View: 723

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"This book considers evolution at different scales. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies, indicate their limitations, and give them orientation"--Provided by publisher.
2005-02-24 By Olivier Gascuel

... an idealized characteristic quantity in a mathematical or statistical model (Ch. 3) parsimony: the idea that simpler solutions are more likely to be correct; often applied as a means of constructing genealogies or phylogenies based ...

Author: Asher D. Cutter

Publisher: Oxford University Press, USA

ISBN: 9780198838944

Category: Genetics

Page: 247

View: 727

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What are the genomic signatures of adaptations in DNA? How often does natural selection dictate changes to DNA? How does the ebb and flow in the abundance of individuals over time get marked onto chromosomes to record genetic history? Molecular population genetics seeks to answer such questions by explaining genetic variation and molecular evolution from micro-evolutionary principles. It provides a way to learn about how evolution works and how it shapes species by incorporating molecular details of DNA as the heritable material. It enables us to understand the logic of how mutations originate, change in abundance in populations, and become fixed as DNA sequence divergence between species. With the revolutionary advances in genomic data acquisition, understanding molecular population genetics is now a fundamental requirement for today's life scientists. These concepts apply in analysis of personal genomics, genome-wide association studies, landscape and conservation genetics, forensics, molecular anthropology, and selection scans. This book introduces, in an accessible way, the bare essentials of the theory and practice of molecular population genetics.
2019 By Asher D. Cutter

8.6 Conclusion The success of a criterion of phylogenetic estimation is undoubtedly influenced by the quality of the ... Hence, families of estimation criteria cohabit in the literature of molecular phylogenetics, by providing different ...

Author: Renato Bruni

Publisher: Springer Science & Business Media

ISBN: 1441968008

Category: Science

Page: 248

View: 725

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An edited volume describing the latest developments in approaching the problem of polymer sequence analysis, with special emphasis on the most relevant biopolymers (peptides and DNA) but not limited to them. The chapters will include peptide sequence analysis, DNA sequence analysis, analysis of biopolymers and nonpolymers, sequence alignment problems, and more.
2010-10-17 By Renato Bruni

enzymes are used in this case, some modification of the mathematical formulas involved is necessary. ... This method is different from the standard PCR in that only a single random oligonucleotide primer (usually about ten nucleotides ...

Author: Masatoshi Nei

Publisher: Oxford University Press

ISBN: 0195350510

Category: Science

Page: 352

View: 525

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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.
2000-07-27 By Masatoshi Nei

Reconstruction of molecular phylogeny and inference of the molecular evolutionary process are considered problems of ... Third, I have prepared a primer on probability and statistics, with an overview of mathematical results used in ...

Author: Ziheng Yang

Publisher: OUP Oxford

ISBN: 9780191023309

Category: Science

Page: 528

View: 711

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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.
2014-05-16 By Ziheng Yang

Papers Related to the Special Year in Mathematical Support for Molecular Biology, 1994-1998 Dimacs Special Year in ... In these methods , a short piece of DNA containing the desired pattern ( the “ probe ” or “ primer ” ) is used to ...

Author: Dimacs Special Year in Mathematical Su

Publisher: American Mathematical Soc.

ISBN: 0821808265

Category: Science

Page: 288

View: 418

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This volume features highlights from the DIMACS Special Year on ``Mathematical Support for Molecular Biology''. Top researchers presented both new research results and comprehensive overviews on the use of mathematics (especially discrete mathematics) and theoretical computer science in molecular biology. The book provides a unique ``snapshot'' of this growing area of study. It will be of interest to both experts and novices seeking information on the state of the research.

Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders. ... The evolutionary and mathematical demography of the turtle Chrysemys picta. ... Molecular Phylogenetics and Evolution 25: 361–371.

Author: Laurie J. Vitt

Publisher: Academic Press

ISBN: 0080921892

Category: Science

Page: 720

View: 148

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This third edition, now fully revised and updated by two of Dr. Zug's colleagues, provides herpetology students and amateur reptile and amphibian keepers with the latest taxonomy and species developments from around the world. Herpetology is a rapidly evolving field, which has contributed to new discoveries in many conceptual areas of biology. The authors build on this progress by updating all chapters with new literature, graphics, and discussions—many of which have changed our thinking. With a new emphasis placed on conservation issues, Herpetology continues to broaden the global coverage from earlier editions, recognizing the burgeoning reptile and amphibian research programs and the plight of many species in all countries and all biomes. New information on the remarkable advances in behavioral, physiological, and phylo-geographical data provide students with the current research they need to advance their education and better prepare their future in herpetology. * The latest taxonomy data * End-of-chapter discussions for classroom use * 90% new photographs, now all in full color for an enhanced visual representation * Most recent information on the exciting and developing herpetological communities in Australia, Europe, Asia, South and North Americas * New emphasis on conservation issues surrounding herpetology
2008-12-15 By Laurie J. Vitt

Mathematical dissertations on a variety of physical and analytical subjects. London, T. Woodward. ... Cladistics: a practical primer on CD-Rom. ... Integrating fossils with molecular phylogenies improves inference of trait evolution.

Author: Richard J. Howarth

Publisher: Springer

ISBN: 9783319573151

Category: Science

Page: 893

View: 219

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This dictionary includes a number of mathematical, statistical and computing terms and their definitions to assist geoscientists and provide guidance on the methods and terminology encountered in the literature. Each technical term used in the explanations can be found in the dictionary which also includes explanations of basics, such as trigonometric functions and logarithms. There are also citations from the relevant literature to show the term’s first use in mathematics, statistics, etc. and its subsequent usage in geosciences.
2017-05-27 By Richard J. Howarth

Jacobs , H. T. , D. J. Elliott , V. B. Math , A. Farquharson . 1988 . ... Effects of primer - template mismatches on the polymerase chain reaction : human immunodeficiency virus type 1 model studies . ... Systematics , Ecology and 152.

Author: Robert J. Van Syoc

Publisher:

ISBN: UCSD:31822016473563

Category: Barnacles

Page: 320

View: 359

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Felsenstein J ( 1988 ) Phylogenies from molecular sequences : inference and reliability . ... Hillis DM ( 1997 ) Primer : phylogenetic analysis Current Biology , 7 , 129–131 . ... Journal of Applied Mathematics , 28 , 35-42 .

Author: North Atlantic Treaty Organization. Scientific Affairs Division

Publisher: IOS Press

ISBN: 9051994400

Category: Science

Page: 313

View: 179

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Each contributor to this publication was asked to examine how molecular genetic tools have contributed to their specific areas of consideration. To increase the practical utility of the book, a summary of software that is available for the anaylsis of data in molecular ecology is included.

Gene genealogies, Variation and Evolution: a Primer in Coalescent Theory by Jotun Hein, and Mikkel Schierup, ... Molecular Phylogenetics C.1 Introduction The main goal in molecular phylogenetics Introduction to Population Genetics 453.

Author: Raúl Rabadán

Publisher: Cambridge University Press

ISBN: 9781107159549

Category: Science

Page:

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An introduction to geometric and topological methods to analyze large scale biological data; includes statistics and genomic applications.
2019-12-31 By Raúl Rabadán

Body shape vs. colour associated initial divergence in the Telmatherina radiation in Lake Matano, Sulawesi, Indonesia. Journal of Evolutionary Biology ... Molecular Phylogenetics and Evolution 38: 426–438. Schliewen, U. K. & B. Klee, ...

Author: Thomas Wilke

Publisher: Springer Science & Business Media

ISBN: 9781402095825

Category: Science

Page: 236

View: 901

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Ancient lakes are exceptional freshwater environments that have continued to exist for hundreds of thousands of years. They have long been recognized as centres of biodiversity and hotspots of evolution. During recent decades, speciation in ancient lakes has emerged as an important and exciting topic in evolutionary biology. The contributions in this volume deal with patterns and processes of biological diversification in three prominent ancient lake systems. Of these, the famous East African Great Lakes already have a strong tradition of evolutionary studies, but the two other systems have so far received much less attention. The exceptional biodiversity of the European sister lakes Ohrid and Prespa of the Balkans has long been known, but has largely been neglected in the international literature until recently. The rich biota and problems of its evolution in the two central lake systems on the Indonesian island of Sulawesi, in turn, have only lately started to draw scientific attention. This volume aims at deepening the awareness of the unusual biological diversity in ancient lakes in general, and of the role of these lakes as natural laboratories for the study of speciation and diversification in particular. It should stimulate further research that will lead to a better understanding of key evolutionary processes in these lakes, and to knowledge that might help in mitigating the deterioration of their diversity in the future.
2009-04-02 By Thomas Wilke

Congruence between molecular and morphological phylogenies. Annu. Rev. Ecol. Syst 24, 153–188. ... Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. ... “The Mathematical Theory of Communication.

Author: David P. Mindell

Publisher: Academic Press

ISBN: 0080527752

Category: Nature

Page: 382

View: 955

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The use of DNA and other biological macromolecules has revolutionized systematic studies of evolutionary history. Methods that use sequences of nucleotides and amino acids are now routinely used as data for addressing evolutionary questions that, although not new questions, have defied description and analysis. The world-renowned contributors use these new methods to unravel particular aspects of the evolutionary history of birds. Avian Molecular Evolution and Systematics presents an overview of the theory and application of molecular systematics, focusing on the phylogeny and evolutionary biology of birds. New, developing areas in the phylogeny of birds at multiple taxonomic areas are covered, as well as methods of analysis for molecular data, evolutionary genetics within and between bird populations, and the application of molecular-based phylogenies to broader questions of evolution. Contains authoritative contributions from leading researchers Discusses the utility of different molecular markers for questions of avian evolution, involving populations and higher-level taxa Applies molecular-based phylogenies of birds and molecular population genetics data to broad questions of organismal and molecular evolution. Compares and contrasts molecular and morphological data sets
1997-05-13 By David P. Mindell

Because many sections of DNA complementary to the primer may occur, the PCR reaction will result in DNA strands of many ... The following is a brief summary of how molecular data may be analyzed in a molecular phylogenetic study .

Author: Michael G. Simpson

Publisher: Academic Press

ISBN: 9780128126288

Category: Science

Page: 896

View: 491

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Plant Systematics, Third Edition, has made substantial contributions to plant systematics courses at the upper-undergraduate and first year graduate level, with the first edition winning The New York Botanical Garden's Henry Allan Gleason Award for outstanding recent publication in plant taxonomy, plant ecology or plant geography. This third edition continues to provide the basis for teaching an introduction to the morphology, evolution and classification of land plants. A foundation of the approach, methods, research goals, evidence and terminology of plant systematics are presented, along with the most recent knowledge of evolutionary relationships of plants and practical information vital to the field. In this new edition, the author includes greatly expanded treatments on families of flowering plants, as well as tropical trees (all with full-color plates), and an updated explanation of maximum likelihood and Bayesian inference algorithms. Chapters on morphology and plant nomenclature have also been enhanced with new material. Covers research developments in plant molecular biology Features clear, detailed cladograms, drawings and photos Includes major revisions to chapters on phylogenetic systematics and plant morphology
2019-10-15 By Michael G. Simpson

... frequent in future, in part because the ever greater availability of sequence information simplifies primer development. ... which can be deciphered by increasingly sophisticated mathematical approaches such as coalescent analysis.

Author: Allan Baker

Publisher: John Wiley & Sons

ISBN: 9781444311419

Category: Science

Page: 352

View: 789

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The incorporation of molecular methods in ecological research has added an exciting new dimension to conventional studies, and opened windows into previously intractable areas of research, at the interface between ecology and genetics. Using these new methods it has now become routine to use genetic markers to study ecological phenomena, from molecular sexing of individuals and parentage of offspring, through to population structure of species and phylogenetic relationships of taxa. These methods have stimulated an explosion of empirical and analytical developments in molecular ecology, which have in turn, increasingly attracted students and professional biologists eager to employ them in their studies. Molecular Methods in Ecology traces the development of molecular ecology by reviewing basic molecular biological techniques and earlier methods such as protein electrophoresis, DNA-DNA hybridisation, restriction analysis of DNA, and DNA fingerprinting. Later chapters review methods using newer classes of markers such as microsatellites, introns, MHC, SSRs and AFLP markers in plants and molecular sexing in animals. The strengths and limitations of methods are discussed and guidance is provided in selecting the most appropriate methods for particular problems in ecology. This book will provide both postgraduates and researchers with a guide to choosing and employing appropriate methodologies for successful research in the field of molecular ecology. Provides up-to-date summaries of the latest molecular approaches in this rapidly expanding field. Gives guidance on the appropriate choice of methods for particular problems in ecology, and their strengths and limitations. Provides brief laboratory protocols for each molecular method and summaries of software available for analysis of data in molecular ecology. Outlines examples of the latest research results from studies of both plants and animals, integrated within the framework of molecular ecology.
2009-04-01 By Allan Baker

2004 The structural basis of DNA flexibility . Travers AA . Philos MODELS , THEORETICAL Jun ; 16 ( 6 ) : 551-01 . ( 29 ref . ) Transact Ser Decision analysis and economic modelling : a primer . Inadomi JM . Math Phys Eng Sci .

Author:

Publisher:

ISBN: OSU:32436011091822

Category: Medicine

Page:

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Molecular Phylogenetics and Evolution, 17(1):58–75, 2000. Motoo Kimura. ... Math. Biosci., 237(1-2):38–48, 2012. ISSN 0025-5564. doi:10.1016/j.mbs.2012.03.001. URL http://dx.doi.org/10. ... A Primer of Real Analytic Functions.

Author: Piotr Zwiernik

Publisher: CRC Press

ISBN: 9781466576223

Category: Mathematics

Page: 245

View: 317

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Semialgebraic Statistics and Latent Tree Models explains how to analyze statistical models with hidden (latent) variables. It takes a systematic, geometric approach to studying the semialgebraic structure of latent tree models.The first part of the book gives a general introduction to key concepts in algebraic statistics, focusing on methods that a
2015-08-21 By Piotr Zwiernik

British Journal of Mathematical and Statistical Psychology 34 : 167–180 . Doolittle , R. F. ( 1986 ) . Of Urfs and Orfs : A Primer on How to Analyze Derived Amino Acid Sequences . Mill Valley , Calif .: University Science Books .

Author: Tao Jiang

Publisher: MIT Press

ISBN: 0262100924

Category: Science

Page: 542

View: 988

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A survey of current topics in computational molecular biology. Computational molecular biology, or bioinformatics, draws on the disciplines of biology, mathematics, statistics, physics, chemistry, computer science, and engineering. It provides the computational support for functional genomics, which links the behavior of cells, organisms, and populations to the information encoded in the genomes, as well as for structural genomics. At the heart of all large-scale and high-throughput biotechnologies, it has a growing impact on health and medicine. This survey of computational molecular biology covers traditional topics such as protein structure modeling and sequence alignment, and more recent ones such as expression data analysis and comparative genomics. It combines algorithmic, statistical, database, and AI-based methods for studying biological problems. The book also contains an introductory chapter, as well as one on general statistical modeling and computational techniques in molecular biology. Each chapter presents a self-contained review of a specific subject. Not for sale in China, including Hong Kong.
2002 By Tao Jiang

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