Detecting Signatures Of Natural Selection In Genetic Data

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Detecting Signatures of Natural Selection in Genetic Data

Author : Aatish Bhatia
Publisher :
ISBN 13 :
Total Pages : 109 pages
Book Rating : 4.:/5 (87 download)

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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.

Identifying and Characterizing the Genomic Signatures of Natural Selection

Author : Roy Ronen
Publisher :
ISBN 13 : 9781321452006
Total Pages : 142 pages
Book Rating : 4.4/5 (52 download)

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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.

Handbook of Statistical Genomics

Author : David J. Balding
Publisher : John Wiley & Sons
ISBN 13 : 1119429250
Total Pages : 1828 pages
Book Rating : 4.1/5 (194 download)

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Book Synopsis Handbook of Statistical Genomics by : David J. Balding

Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.

Statistical Population Genomics

Author : Julien Y Dutheil
Publisher :
ISBN 13 : 9781013271403
Total Pages : 464 pages
Book Rating : 4.2/5 (714 download)

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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.

Natural Selection

Author : Mario A. Fares
Publisher : CRC Press
ISBN 13 : 1482263726
Total Pages : 276 pages
Book Rating : 4.4/5 (822 download)

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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.

Adaptive and Neutral Evolutionary Insights from Statistical Analyses of Population Genetic Data

Author : Julie Marie Granka
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (841 download)

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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.

Mathematical Population Genetics 1

Author : Warren J. Ewens
Publisher : Springer Science & Business Media
ISBN 13 : 038721822X
Total Pages : 435 pages
Book Rating : 4.3/5 (872 download)

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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.

Elements of Evolutionary Genetics

Author : Brian Charlesworth
Publisher : Roberts
ISBN 13 :
Total Pages : 776 pages
Book Rating : 4.F/5 ( download)

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Book Synopsis Elements of Evolutionary Genetics by : Brian Charlesworth

Download or read book Elements of Evolutionary Genetics written by Brian Charlesworth and published by Roberts. This book was released on 2010-02-03 with total page 776 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook shows readers how models of the genetic processes involved in evolution are made (including natural selection, migration, mutation, and genetic drift in finite populations), and how the models are used to interpret classical and molecular genetic data. The material is intended for advanced level undergraduate courses in genetics and evolutionary biology, graduate students in evolutionary biology and human genetics, and researchers in related fields who wish to learn evolutionary genetics. The topics covered include genetic variation, DNA sequence variability and its measurement, the different types of natural selection and their effects (e.g. the maintenance of variation, directional selection, and adaptation), the interactions between selection and mutation or migration, the description and analysis of variation at multiple sites in the genome, genetic drift, and the effects of spatial structure.

The Genetics of Human Populations

Author : Luigi Luca Cavalli-Sforza
Publisher : Courier Corporation
ISBN 13 : 0486406938
Total Pages : 994 pages
Book Rating : 4.4/5 (864 download)

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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.

Estimating Evolutionary Parameters and Detecting Signals of Natural Selection from Genetic Data

Author : Gaurav Bhatia
Publisher :
ISBN 13 :
Total Pages : 86 pages
Book Rating : 4.:/5 (89 download)

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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.

Detecting Natural Selection in Human Populations

Author : Anna diRienzo
Publisher :
ISBN 13 :
Total Pages : 0 pages
Book Rating : 4.:/5 (137 download)

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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.

Mathematical Population Genetics 1

Author : Warren J. Ewens
Publisher : Springer Science & Business Media
ISBN 13 : 9780387201917
Total Pages : 448 pages
Book Rating : 4.2/5 (19 download)

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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 2004-01-09 with total page 448 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.

Evolution and Selection of Quantitative Traits

Author : Bruce Walsh
Publisher : Oxford University Press
ISBN 13 : 0192566644
Total Pages : 1504 pages
Book Rating : 4.1/5 (925 download)

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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.

Demographic Methods Across the Tree of Life

Author : Roberto Salguero-Gomez
Publisher : Oxford University Press
ISBN 13 : 0198838603
Total Pages : 401 pages
Book Rating : 4.1/5 (988 download)

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Book Synopsis Demographic Methods Across the Tree of Life by : Roberto Salguero-Gomez

Download or read book Demographic Methods Across the Tree of Life written by Roberto Salguero-Gomez and published by Oxford University Press. This book was released on 2021 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: Demography is everywhere in our lives: from birth to death. Indeed, the universal currencies of survival, development, reproduction, and recruitment shape the performance of all species, from microbes to humans. The number of techniques for demographic data acquisition and analyses across the entire tree of life (microbes, fungi, plants, and animals) has drastically increased in recent decades. These developments have been partially facilitated by the advent of technologies such as GIS and drones, as well as analytical methods including Bayesian statistics and high-throughput molecular analyses. However, despite the universality of demography and the significant research potential that could emerge from unifying: (i) questions across taxa, (ii) data collection protocols, and (iii) analytical tools, demographic methods to date have remained taxonomically siloed and methodologically disintegrated. This is the first book to attempt a truly unified approach to demography and population ecology in order to address a wide range of questions in ecology, evolution, and conservation biology across the entire spectrum of life. This novel book provides the reader with the fundamentals of data collection, model construction, analyses, and interpretation across a wide repertoire of demographic techniques and protocols. It introduces the novice demographer to a broad range of demographic methods, including abundance-based models, life tables, matrix population models, integral projection models, integrated population models, individual based models, and more. Through the careful integration of data collection methods, analytical approaches, and applications, clearly guided throughout with fully reproducible R scripts, the book provides an up-to-date and authoritative overview of the most popular and effective demographic tools. Demographic Methods across the Tree of Life is aimed at graduate students and professional researchers in the fields of demography, ecology, animal behaviour, genetics, evolutionary biology, mathematical biology, and wildlife management.

Population Genetics, Molecular Evolution, and the Neutral Theory

Author : Motoo Kimura
Publisher : University of Chicago Press
ISBN 13 : 9780226435633
Total Pages : 736 pages
Book Rating : 4.4/5 (356 download)

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Book Synopsis Population Genetics, Molecular Evolution, and the Neutral Theory by : Motoo Kimura

Download or read book Population Genetics, Molecular Evolution, and the Neutral Theory written by Motoo Kimura and published by University of Chicago Press. This book was released on 1994 with total page 736 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Conservation and the Genetics of Populations

Author : Fred W. Allendorf
Publisher : John Wiley & Sons
ISBN 13 : 1444309056
Total Pages : 664 pages
Book Rating : 4.4/5 (443 download)

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Book Synopsis Conservation and the Genetics of Populations by : Fred W. Allendorf

Download or read book Conservation and the Genetics of Populations written by Fred W. Allendorf and published by John Wiley & Sons. This book was released on 2009-03-12 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Conservation and the Genetics of Populations gives acomprehensive overview of the essential background, concepts, andtools needed to understand how genetic information can be used todevelop conservation plans for species threatened withextinction. Provides a thorough understanding of the genetic basis ofbiological problems in conservation. Uses a balance of data and theory, and basic and appliedresearch, with examples taken from both the animal and plantkingdoms. An associated website contains example data sets and softwareprograms to illustrate population genetic processes and methods ofdata analysis. Discussion questions and problems are included at the end ofeach chapter to aid understanding. Features Guest Boxes written by leading people in the fieldincluding James F. Crow, Nancy FitzSimmons, Robert C. Lacy, MichaelW. Nachman, Michael E. Soule, Andrea Taylor, Loren H. Rieseberg,R.C. Vrijenhoek, Lisette Waits, Robin S. Waples and AndrewYoung. Supplementary information designed to support Conservationand the Genetics of Populations including: Downloadable sample chapter Answers to questions and problems Data sets illustrating problems from the book Data analysis software programs Website links An Instructor manual CD-ROM for this title is available. Pleasecontact our Higher Education team at ahref="mailto:[email protected]"[email protected]/afor more information.

Linkage Disequilibrium and Association Mapping

Author : Andrew R. Collins
Publisher : Springer Science & Business Media
ISBN 13 : 1597453897
Total Pages : 529 pages
Book Rating : 4.5/5 (974 download)

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Book Synopsis Linkage Disequilibrium and Association Mapping by : Andrew R. Collins

Download or read book Linkage Disequilibrium and Association Mapping written by Andrew R. Collins and published by Springer Science & Business Media. This book was released on 2008-02-05 with total page 529 pages. Available in PDF, EPUB and Kindle. Book excerpt: As researchers continue to make enormous progress in mapping disease genes, exciting, novel, and complex analyses have emerged. In this book, scientists from around the world, who are leaders in this field, contribute their vast experience and expertise to produce a comprehensive and fascinating text for researchers and clinicians alike. They provide cutting-edge analysis of the most up-to-date and preeminent information available.