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Branching Processes and Neutral Evolution

Branching Processes and Neutral Evolution
Author: Ziad Taib
Publisher: Springer Science & Business Media
Total Pages: 120
Release: 2013-03-09
Genre: Mathematics
ISBN: 3642515363

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The Galton-Watson branching process has its roots in the problem of extinction of family names which was given a precise formulation by F. Galton as problem 4001 in the Educational Times (17, 1873). In 1875, an attempt to solve this problem was made by H. W. Watson but as it turned out, his conclusion was incorrect. Half a century later, R. A. Fisher made use of the Galton-Watson process to determine the extinction probability of the progeny of a mutant gene. However, it was J. B. S. Haldane who finally gave the first sketch of the correct conclusion. J. B. S. Haldane also predicted that mathematical genetics might some day develop into a "respectable branch of applied mathematics" (quoted in M. Kimura & T. Ohta, Theoretical Aspects of Population Genetics. Princeton, 1971). Since the time of Fisher and Haldane, the two fields of branching processes and mathematical genetics have attained a high degree of sophistication but in different directions. This monograph is a first attempt to apply the current state of knowledge concerning single-type branching processes to a particular area of mathematical genetics: neutral evolution. The reader is assumed to be familiar with some of the concepts of probability theory, but no particular knowledge of branching processes is required. Following the advice of an anonymous referee, I have enlarged my original version of the introduction (Chapter Zero) in order to make it accessible to a larger audience. G6teborg, Sweden, November 1991.


Population Genetics, Molecular Evolution, and the Neutral Theory

Population Genetics, Molecular Evolution, and the Neutral Theory
Author: Motoo Kimura
Publisher: University of Chicago Press
Total Pages: 736
Release: 1994
Genre: Science
ISBN: 9780226435633

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One of this century's leading evolutionary biologists, Motoo Kimura revolutionized the field with his random drift theory of molecular evolution—the neutral theory—and his groundbreaking theoretical work in population genetics. This volume collects 57 of Kimura's most important papers and covers forty years of his diverse and original contributions to our understanding of how genetic variation affects evolutionary change. Kimura's neutral theory, first presented in 1968, challenged the notion that natural selection was the sole directive force in evolution. Arguing that mutations and random drift account for variations at the level of DNA and amino acids, Kimura advanced a theory of evolutionary change that was strongly challenged at first and that eventually earned the respect and interest of evolutionary biologists throughout the world. This volume includes the seminal papers on the neutral theory, as well as many others that cover such topics as population structure, variable selection intensity, the genetics of quantitative characters, inbreeding systems, and reversibility of changes by random drift. Background essays by Naoyuki Takahata examine Kimura's work in relation to its effects and recent developments in each area.


Branching Processes in Biology

Branching Processes in Biology
Author: Marek Kimmel
Publisher: Springer Science & Business Media
Total Pages: 242
Release: 2002-05-10
Genre: Mathematics
ISBN: 038795340X

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Biological examples of branching processes from molecular and cellular biology are introduced in this volume, as well as from the fields of human evolution and medicine. It will interest scientists who work in quantitative modeling of biological systems, particularly probabilists, mathematical biologists, and others. 54 illustrations.


The Neutral Theory of Molecular Evolution

The Neutral Theory of Molecular Evolution
Author: Motoo Kimura
Publisher: Cambridge University Press
Total Pages: 388
Release: 1983
Genre: Science
ISBN: 9780521317931

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This book is the first comprehensive treatment of this subject.


Branching Processes

Branching Processes
Author: Patsy Haccou
Publisher: Cambridge University Press
Total Pages: 332
Release: 2007-11-05
Genre: Science
ISBN: 9780521539852

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Biology takes a special place among the other natural sciences because biological units, be they pieces of DNA, cells or organisms, reproduce more or less faithfully. As for any other biological processes, reproduction has a large random component. The theory of branching processes was developed especially as a mathematical counterpart to this most fundamental of biological processes. This active and rich research area allows us to make predictions about both extinction risks and the development of population composition, and also uncovers aspects of a population's history from its current genetic composition. Branching processes play an increasingly important role in models of genetics, molecular biology, microbiology, ecology and evolutionary theory. This book presents this body of mathematical ideas for a biological audience, but should also be enjoyable to mathematicians.


Stochastic Processes: Modeling and Simulation

Stochastic Processes: Modeling and Simulation
Author: D N Shanbhag
Publisher: Gulf Professional Publishing
Total Pages: 1028
Release: 2003-02-24
Genre: Mathematics
ISBN: 9780444500137

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This sequel to volume 19 of Handbook on Statistics on Stochastic Processes: Modelling and Simulation is concerned mainly with the theme of reviewing and, in some cases, unifying with new ideas the different lines of research and developments in stochastic processes of applied flavour. This volume consists of 23 chapters addressing various topics in stochastic processes. These include, among others, those on manufacturing systems, random graphs, reliability, epidemic modelling, self-similar processes, empirical processes, time series models, extreme value therapy, applications of Markov chains, modelling with Monte Carlo techniques, and stochastic processes in subjects such as engineering, telecommunications, biology, astronomy and chemistry. particular with modelling, simulation techniques and numerical methods concerned with stochastic processes. The scope of the project involving this volume as well as volume 19 is already clarified in the preface of volume 19. The present volume completes the aim of the project and should serve as an aid to students, teachers, researchers and practitioners interested in applied stochastic processes.


Stochastic Processes in Genetics and Evolution

Stochastic Processes in Genetics and Evolution
Author: Charles J. Mode
Publisher: World Scientific
Total Pages: 695
Release: 2012
Genre: Mathematics
ISBN: 9814350672

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The scope of this book is the field of evolutionary genetics. The book contains new methods for simulating evolution at the genomic level. It sets out applications using up to date Monte Carlo simulation methods applied in classical population genetics, and sets out new fields of quantifying mutation and selection at the Mendelian level. A serious limitation of Wright-Fisher process, the assumption that population size is constant, motivated the introduction of self regulating branching processes in this book. While providing a short review of the principles of probability and its application and using computer intensive methods whilst applying these principles, this book explains how it is possible to derive new formulas expressed in terms of matrix algebra providing new insights into the classical Wright-Fisher processes of evolutionary genetics. Also covered are the development of new methods for studying genetics and evolution, simulating nucleotide substitutions of a DNA molecule and on self regulating branching processes. Components of natural selection are studied in terms of reproductive success of each genotype whilst also studying the differential ability of genotypes to compete for resources and sexual selection. The concept of the gene is also reviewed in this book, and it provides a current definition of a gene based on very recent experiments with micro-array technologies. A development of stochastic models for simulating the evolution of model genomes concludes the studies in this book. Deserving of a place on the book shelves of workers in biomathematics, applied probability, stochastic processes and statistics, as well as in bioinformatics and phylogenetics, it will also be relevant to those interested in computer simulation, and evolutionary biologists interested in quantitative methods.


Introduction to Evolutionary Genomics

Introduction to Evolutionary Genomics
Author: Naruya Saitou
Publisher: Springer
Total Pages: 504
Release: 2018-10-25
Genre: Computers
ISBN: 331992642X

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This authoritative textbook/reference presents a comprehensive introduction to the field of evolutionary genomics. The opening chapters describe the fundamental concepts in molecular biology and genome evolution for readers without any prior background in this area. This is followed by a detailed examination of genome evolution in various different groups of organisms. The text then concludes with a review of practical methods essential to researchers in the field. This updated and revised new edition also features historical perspectives on contributions to evolutionary genomics from related fields such as molecular evolution, genetics, and numerical taxonomy. Topics and features: introduces the basics of molecular biology, covering protein structure and diversity, as well as DNA replication, transcription, and translation; examines the phylogenetic relationships of DNA sequences, and the processes of mutation, neutral evolution, and natural selection; presents a brief evolutionary history of life, surveying the key features of the genomes of prokaryotes, eukaryotes, viruses and phages, vertebrates, and humans; reviews the various biological “omic” databases, and discusses the analysis of homologous nucleotide and amino acid sequences; provides an overview of the experimental sequencing of genomes and transcriptomes, and the construction of phylogenetic trees; describes methods for estimating of evolutionary distances, and performing studies of population genetics; supplies additional supporting material at an associated website. Serving as an indispensable textbook for graduate and advanced undergraduate courses on evolutionary genomics, this accessible overview will also prove invaluable to researchers from both computer science and the biological sciences seeking a primer on the field.


Theoretical and Computational Methods in Genome Research

Theoretical and Computational Methods in Genome Research
Author: Sándor Suhai
Publisher: Springer Science & Business Media
Total Pages: 332
Release: 2012-12-06
Genre: Science
ISBN: 1461559030

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The application ofcomputational methods to solve scientific and practical problems in genome research created a new interdisciplinary area that transcends boundaries tradi tionally separating genetics, biology, mathematics, physics, and computer science. Com puters have, of course, been intensively used in the field of life sciences for many years, even before genome research started, to store and analyze DNA or protein sequences; to explore and model the three-dimensional structure, the dynamics, and the function of biopolymers; to compute genetic linkage or evolutionary processes; and more. The rapid development of new molecular and genetic technologies, combined with ambitious goals to explore the structure and function ofgenomes ofhigher organisms, has generated, how ever, not only a huge and exponentially increasing body of data but also a new class of scientific questions. The nature and complexity of these questions will also require, be yond establishing a new kind ofalliance between experimental and theoretical disciplines, the development of new generations both in computer software and hardware technolo gies. New theoretical procedures, combined with powerful computational facilities, will substantially extend the horizon of problems that genome research can attack with suc cess. Many of us still feel that computational models rationalizing experimental findings in genome research fulfill their promises more slowly than desired. There is also an uncer tainty concerning the real position of a "theoretical genome research" in the network of established disciplines integrating their efforts in this field.