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Estimating Evolutionary Parameters And Detecting Signals Of Natural Selection From Genetic Data
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Book Synopsis Estimating Evolutionary Parameters and Detecting Signals of Natural Selection from Genetic Data by : Gaurav Bhatia
Download or read book Estimating Evolutionary Parameters and Detecting Signals of Natural Selection from Genetic Data written by Gaurav Bhatia and published by . This book was released on 2014 with total page 86 pages. Available in PDF, EPUB and Kindle. Book excerpt: Even prior to the elucidation of the structure of DNA, the theoretical foundations of population genetics had been well developed. Advances made by Sewall Wright, John B.S. Haldane, and Ronald A. Fisher form the basis with which we understand the statistical dynamics of evolution and inheritance. Using this foundation, recent advances in DNA profiling technologies have enabled genome-wide analysis of thousands of individuals from a diverse array of human populations. These new analyses can answer fundamental questions about human population differences, natural selection, and admixture. However, with this deluge of newly available data, confusion about statistical methods may lead to misleading conclusions about human population history and natural selection. We view it as imperative to put analyses of population differences on sound statistical footing. In the course of this thesis, we have developed methods and reanalyzed existing results in two related areas: the detection of natural selection and estimation of genetic distance. Throughout our work, we have strived for statistical rigor, attempting to understand variation in previously reported results and provide a resource for other researchers in our field. Where necessary, we have made simplifying assumptions about evolutionary processes but have attempted to state these clearly and validate their reasonableness using simulations. Our efforts have culminated in three projects that will be described in the subsequent chapters: (1) A model based approach to detect natural selection in 3 populations (2) A protocol to generate consistent estimates of FST and, (3) Reanalysis of previously reports of selection in African Americans since the arrival of their ancestors in the Americas. We note that our work is just part of a rich literature on population and evolutionary genetics. We have attempted to cite this literature in detail and have published our own methods to enable others to utilize and improve upon them.
Book Synopsis Evolutionary Genetics by : Glenn-Peter Sætre
Download or read book Evolutionary Genetics written by Glenn-Peter Sætre and published by Oxford University Press, USA. This book was released on 2019-05 with total page 327 pages. Available in PDF, EPUB and Kindle. Book excerpt: Evolutionary genetics is the study of how genetic variation leads to evolutionary change. With the recent explosion in the availability of whole genome sequence data, vast quantities of genetic data are being generated at an ever-increasing pace with the result that programming has become an essential tool for researchers. Most importantly, a thorough understanding of evolutionary principles is essential for making sense of this genetic data. This up-to-date textbook covers all the major components of modern evolutionary genetics, carefully explaining fundamental processes such as mutation, natural selection, genetic drift, and speciation, together with their consequences. The book also draws on a rich literature of exciting and inspiring examples to demonstrate the diversity of evolutionary research, including an emphasis on how evolution and selection has shaped our own species. Furthermore, at the end of each chapter, study questions are provided to motivate the reader to think and reflect on the concepts introduced. Practical experience is essential when it comes to developing an understanding of how to use genetic and genomic data to analyze and address interesting questions in the life sciences and how to interpret results in meaningful ways. In addition to the main text, a series of online tutorials using the R language serves as an introduction to programming, statistics, and the analysis of evolutionary genetic data. The R environment stands out as an ideal all-purpose, open source platform to handle and analyze such data. The book and its online materials take full advantage of the authors' own experience in working in a post-genomic revolution world, and introduce readers to the plethora of molecular and analytical methods that have only recently become available.
Book Synopsis Evolution and Selection of Quantitative Traits by : Bruce Walsh
Download or read book Evolution and Selection of Quantitative Traits written by Bruce Walsh and published by Oxford University Press. This book was released on 2018-06-21 with total page 1504 pages. Available in PDF, EPUB and Kindle. Book excerpt: Quantitative traits-be they morphological or physiological characters, aspects of behavior, or genome-level features such as the amount of RNA or protein expression for a specific gene-usually show considerable variation within and among populations. Quantitative genetics, also referred to as the genetics of complex traits, is the study of such characters and is based on mathematical models of evolution in which many genes influence the trait and in which non-genetic factors may also be important. Evolution and Selection of Quantitative Traits presents a holistic treatment of the subject, showing the interplay between theory and data with extensive discussions on statistical issues relating to the estimation of the biologically relevant parameters for these models. Quantitative genetics is viewed as the bridge between complex mathematical models of trait evolution and real-world data, and the authors have clearly framed their treatment as such. This is the second volume in a planned trilogy that summarizes the modern field of quantitative genetics, informed by empirical observations from wide-ranging fields (agriculture, evolution, ecology, and human biology) as well as population genetics, statistical theory, mathematical modeling, genetics, and genomics. Whilst volume 1 (1998) dealt with the genetics of such traits, the main focus of volume 2 is on their evolution, with a special emphasis on detecting selection (ranging from the use of genomic and historical data through to ecological field data) and examining its consequences.
Book Synopsis Natural Selection by : Mario A. Fares
Download or read book Natural Selection written by Mario A. Fares and published by CRC Press. This book was released on 2014-11-21 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book summarizes the knowledge in the field of methods to identify signatures of natural selection. A number of mathematical models and methods have been designed to identify the fingerprints of natural selection on genes and genomes. Such methods are provided in a simple and direct way so that students of different disciplines can navigate through molecular fitness landscapes using complex methods with a basic knowledge on bioinformatics. A collection of the main methods to detect selection in protein-coding genes and amino acid sequences is given at different levels of complexity, from nucleotides to proteins and molecular networks. The importance of identifying natural selection in genes and genomes through the methods described in this book transcends the bioinformatics and computational biology fields, presenting applications for experimental biologists in a straightforward and understandable way.
Book Synopsis Identifying and Characterizing the Genomic Signatures of Natural Selection by : Roy Ronen
Download or read book Identifying and Characterizing the Genomic Signatures of Natural Selection written by Roy Ronen and published by . This book was released on 2014 with total page 142 pages. Available in PDF, EPUB and Kindle. Book excerpt: Despite being founded in the early 1920's, the field of Population and Evolutionary Genetics is currently in its second life. This is primarily driven by the recent data influx from genomic studies of ever-increasing size. The shear amount and complexity of data produced by these studies is also creating a need for improved computational techniques to be used for analysis and inference. In this thesis, I present three computational methods that are aimed at improving our understanding of genetic variation in natural populations. First, I present an algorithm for improving the accuracy of genome assemblies using the positional de Bruijn graph. I show that, using the original sequence reads in conjunction with a novel data structure, I can significantly improve the accuracy of assembled draft genomes. Necessarily, this leads to improved accuracy of all downstream inferences that use the draft as a reference, including gene discovery, transcript expression, variant calling, and many others. Second, I describe a computational framework that uses supervised learning of mutation frequency profiles to identify genomic regions impacted by positive natural selection. This is desirable, as it allows pinpointing and understanding the mechanisms responsible for adaptive traits, such as lactose tolerance in northern European populations, hypoxia tolerance in high altitude populations, and malaria resistance in African populations. Extending the widely used theoretical framework of the site frequency spectrum (SFS), I show that higher power to detect selection is achieved by training parameter-specific models of the SFS. I further show that these models can be generalized, allowing their use without prior knowledge. Last, I describe a new statistic that naturally captures many of the properties shared by haplotypes carrying an adaptive allele. I provide a theoretical model for the behavior of the statistic under different demographic and evolutionary scenarios, and validate the model using simulated data. Using this framework, I develop an algorithm that - given a region we know to be under positive selection - predicts carriers of the adaptive mutation without knowing its position. I demonstrate its high accuracy on simulated data, as well as on genetic data from well-known instances of positive selection in human populations.
Book Synopsis Explorations in Studying Natural Selection by : Weiwei Zhai
Download or read book Explorations in Studying Natural Selection written by Weiwei Zhai and published by . This book was released on 2008 with total page 236 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Evolutionary Genetics written by and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Adaptive and Neutral Evolutionary Insights from Statistical Analyses of Population Genetic Data by : Julie Marie Granka
Download or read book Adaptive and Neutral Evolutionary Insights from Statistical Analyses of Population Genetic Data written by Julie Marie Granka and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Organismic evolution involves both selective and neutral forces, although their relative contributions are often unknown. This thesis proposes novel statistical methods for analyzing genetic data from a variety of organisms, including yeast, Mycobacterium tuberculosis, and humans. The chapters of this thesis provide complimentary perspectives on the relative roles of selection and neutrality, from the molecular to the population level, and present various statistical tools for genetic data analysis. Chapter 2 proposes a maximum-likelihood based method with which to classify and identify interactions, or epistasis, between pairs of genes. Chapter 3 details a study of genetic data from Mycobacterium tuberculosis isolated from human Aboriginal Canadian communities; our analyses suggest that the bacterium spread to these communities via the Canadian fur trade in the 18th and 19th centuries. Chapter 4 discusses the detection of signatures of natural selection in the genomes of 12 diverse African human populations, and proposes novel considerations for identifying biological functions under selection and for comparing signals of selection between populations. Finally, Chapter 5 details the inference of the genetic basis and evolutionary history of light skin pigmentation and short stature in the genetically diverse ≠Khomani Bushmen of the Kalahari Desert of South Africa, believed to be one of the world's most ancient human populations. These chapters emphasize that a more complete understanding of the evolutionary history of humans and other organisms requires not only the consideration of neutral and selective processes, but also both phenotypic and genetic information. The statistical methods and approaches presented in the following chapters have the potential to improve inferences of natural selection and demography from genetic data, as well as provide insight into the relative roles of both.
Book Synopsis Mathematical Population Genetics 1 by : Warren J. Ewens
Download or read book Mathematical Population Genetics 1 written by Warren J. Ewens and published by Springer Science & Business Media. This book was released on 2012-10-01 with total page 435 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first of a planned two-volume work discussing the mathematical aspects of population genetics with an emphasis on evolutionary theory. This volume draws heavily from the author’s 1979 classic, but it has been revised and expanded to include recent topics which follow naturally from the treatment in the earlier edition, such as the theory of molecular population genetics.
Book Synopsis Detecting Signatures of Natural Selection in Genetic Data by : Aatish Bhatia
Download or read book Detecting Signatures of Natural Selection in Genetic Data written by Aatish Bhatia and published by . This book was released on 2013 with total page 109 pages. Available in PDF, EPUB and Kindle. Book excerpt: I report on three studies where I identify signatures of natural selection in humans, and dissect the genetic architecture of complex phenotypic traits in yeast. In chapter 2, I discuss the results of a quantitative trait mapping study, where we showed that yeast growth can be characterized by multiple biologically-relevant growth parameters obtained by fitting yeast growth OD data to a sigmoid function. We identified quantita- tive trait loci (QTL) and gene-gene interactions driving variation in these yeast growth parameters. We analyzed the environment dependence of these QTLs and gene-gene interactions, and identified a common gene, FLO8, which interacts with other genes in an environment specific fashion to affect distinct growth phenotypes. In chapter 3, I describe our published study where we applied quantitative trait locus mapping to wildtype yeast strains, and identified linked clusters of genetic variants that contributed to variation in the sporulation efficiency of these strains. In chapter 4, I describe our work on identifying signatures of natural selection in the human lineage, specifically in the Maasai people in East Africa. Our work suggests that the Maasai have under- gone recent diet induced positive natural selection that may confer protection against hyperlipidemia and cardiac diseases.
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.
Book Synopsis Natural Selection in Human Populations by : Carl Jay Bajema
Download or read book Natural Selection in Human Populations written by Carl Jay Bajema and published by John Wiley & Sons. This book was released on 1971 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Detecting Natural Selection in Human Populations by : Anna diRienzo
Download or read book Detecting Natural Selection in Human Populations written by Anna diRienzo and published by . This book was released on 2008 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Patterns of DNA sequence variation in the genome contain a record of past selective events. The ability to collect increasingly large data sets of polymorphisms has allowed investigators to perform hypothesis-driven studies of candidate genes as well as genome-wide scans for signatures of adaptations. This genetic approach to the study of natural selection has identified many signals consistent with predictions from anthropological studies. Selective pressures related to variation in climate, diet and pathogen exposure have left strong marks on patterns of human variation. Additional signals of adaptations are observed in genes involved in chemosensory perception and reproduction. Several ongoing projects aim at sequencing the complete genome of 1000 individuals from different human populations. These large-scale projects will provide data for more complete genome scans of selection, but more focused studies aimed at testing specific hypotheses will continue to hold an important place in elucidating the history of adaptations in humans.
Book Synopsis The Statistics of Natural Selection on Animal Populations by : Bryan F. J. Manly
Download or read book The Statistics of Natural Selection on Animal Populations written by Bryan F. J. Manly and published by Springer. This book was released on 1985-09-19 with total page 508 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the concluding chapter of his famous book on the theory of evolution by natural selection, Charles Darwin (1859) remarked that: When the views entertained in this volume on the origin of species, or when analogous views are generally admitted, we can dimly foresee that there will be a considerable revolution in natural history. This proved, of course, to be completely correct. At present there is a great divergence of opinion about the general importance of natural selection in the evolutionary process. Nevertheless, biologists are, on the whole, united in their acceptance of the potential power of selection in changing populations. Given this situation, it is not surprising to find that many attempts to detect the effects of natural selection have been made since the time of Darwin. This area of study has been called ecological genetics. It involves the collection of data of various kinds and, in many cases, the development of special methods for analysing these data. This book is a summary of methods for data analysis, concentrating on those that are applicable to animal populations, particularly wild populations.
Book Synopsis Stochastic Processes in Genetics and Evolution by : Charles J. Mode
Download or read book Stochastic Processes in Genetics and Evolution written by Charles J. Mode and published by World Scientific. This book was released on 2012 with total page 695 pages. Available in PDF, EPUB and Kindle. Book excerpt: Prologue; Acknowledgments; Contents; 1. An Introduction to Mathematical Probability with Applications in Mendelian Genetics; 1.1 Introduction; 1.2 Mathematical Probability in Mendelian Genetics; 1.3 Examples of Finite Probability Spaces; Example 1.3.1: An Equal Frequency Model; Example 1.3.2: Partitions of an Abstract Set; Example 1.3.3: A Deterministic Case; Example 1.3.4: Inheritance of Eye Color and Sex; 1.4 Elementary Combinatorial Analysis; 1.5 The Binomial Distribution; Example 1.5.1: Distribution of Boys and Girls in Families of Size N.
Book Synopsis Computational Molecular Evolution by : Ziheng Yang
Download or read book Computational Molecular Evolution written by Ziheng Yang and published by Oxford University Press, USA. This book was released on 2006-10-05 with total page 374 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis The Genetics of Human Populations by : Luigi Luca Cavalli-Sforza
Download or read book The Genetics of Human Populations written by Luigi Luca Cavalli-Sforza and published by Courier Corporation. This book was released on 1999-01-01 with total page 994 pages. Available in PDF, EPUB and Kindle. Book excerpt: Comprehensive, advanced treatment of nature and source of inherited characteristics, with treatment of mathematical techniques. Mendelian populations, mutations, polymorphisms, genetic demography, much more. Emphasizes interpretation of data in relation to theoretical models.
