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Author: Samuel A. Cushman
Publisher: Frontiers Media SA
ISBN: 2832530133
Category : Science
Languages : en
Pages : 149
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Book Description
Author: Samuel A. Cushman
Publisher: Frontiers Media SA
ISBN: 2832530133
Category : Science
Languages : en
Pages : 149
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Book Description
Author: Richard D. Emes
Publisher: Frontiers Media SA
ISBN: 2832531733
Category : Science
Languages : en
Pages : 195
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Book Description
This Research Topic is part of the Insights in Frontiers in Genetics series. Other titles in the series are: Genetics, Insights in Evolutionary and Population Genetics: 2022 Genetics, Insights in Livestock Genomics: 2022 Genetics, Insights in Epigenomics and Epigenetics: 2022 Genetics, Insights in Behavioral and Psychiatric Genetics: 2022 Genetics, Insights in Neurogenomics: 2022 Genetics, Insights in Genomic Assay Technology: 2022 Genetics, Insights in Genetics of Common and Rare Diseases: 2022 We are now entering the third decade of the 21st Century, and, especially in the last years, the achievements made by scientists have been exceptional, leading to major advancements in the fast-growing field of Genetics. Frontiers have organized a series of Research Topics to highlight the latest advancements in research across the field of Computational Genomics, with articles from the members of our accomplished Editorial Boards. This editorial initiative of particular relevance, led by Prof Richard Emes, Specialty Chief Editor of the Computational Genomics section, together with Dr. Pirooznia and Dr Zou, focused on new insights, novel developments, current challenges, latest discoveries, recent advances, and future perspectives in the field of Computational Genomics. The Research Topic solicits brief, forward-looking contributions from the editorial board members that describe the state of the art, outlining recent developments and major accomplishments that have been achieved and that need to occur to move the field forward. Authors are encouraged to identify the greatest challenges in the sub-disciplines, and how to address those challenges.
Author: John H. Gillespie
Publisher:
ISBN:
Category : Science
Languages : en
Pages : 196
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Book Description
"In a species with a million individuals," writes John H. Gillespie, "it takes roughly a million generations for genetic drift to change allele frequencies appreciably. There is no conceivable way of verifying that genetic drift changes allele frequencies in most natural populations. Our understanding that it does is entirely theoretical. Most population geneticists are not only comfortable with this state of affairs, but revel in the fact that they can demonstrate on the back of an envelope, rather than in the laboratory, how an important evolutionary force operates." Longer than the back of an envelope but more concise than many books on the subject, this brief introduction to the field of population genetics offers students and researchers an overview of a discipline that is of growing importance. Chapter topics include genetic drift; natural selection; non-random mating, quantitative genetics; and the evolutionary advantage of sex. While each chapter treats a specific topic or problem in genetics, the common thread throughout the book is what Gillespie calls "the main obsession of our field," the recurring question, "Why is there so much genetic variation in natural populations?" "Population genetics remains the central intellectual connection between genetics and evolution. As genetics becomes integral to all aspects of biology, the unifying nature of evolutionary studies rests more and more on population genetics. This book lays out much of the foundation of population genetics augmented with interesting particulars and conceptual insight. Population genetics involves ideas that are quantitative and often difficult for biology undergraduates, but Professor Gillespie offershis characteristically clear thinking and articulate explanations." -- Charles Langley, University of California-Davis
Author: Gerdina de Jong
Publisher: Springer Science & Business Media
ISBN: 3642730698
Category : Science
Languages : en
Pages : 290
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Book Description
At least since the 1940s neo-Darwinism has prevailed as the consensus view in the study of evolution. The mechanism of evolution in this view is natural selection leading to adaptation, working on a substrate of adapta tionally random mutations. As both the study of genetic variation in natural populations, and the study of the mathematical equations of selec tion are reckoned to a field called population genetics, population genetics came to form the core in the theory of evolution. So much so, that the fact that there is more to the theory of evolution than population genetics became somewhat obscured. The genetics of the evolutionary process, or the genetics of evolutionary change, came close to being all of evolutionary biology. In the last 10 years, this dominating position of population genetics within evolutionary biology has been challenged. In evolutionary ecology, optimization theory proved more useful than population genetics for interesting predictions, especially of life history strategies. From develop mental biology, constraints in development and the role of internal regula tion were emphasized. From paleobiology, a proposal was put forward to describe the fossil record and the evolutionary process as a series of punc tuated equilibria; thus exhorting population geneticists to give a plausible account of how such might come about. All these developments tend to obscure the central role of population genetics in evolutionary biology.
Author: Viktor T. Koven
Publisher: Nova Publishers
ISBN: 9781604564495
Category : Science
Languages : en
Pages : 384
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Book Description
Population genetics is the study of the allele frequency distribution and change under the influence of the four evolutionary forces: natural selection, genetic drift, mutation and gene flow. It also takes account of population subdivision and population structure in space. This book presents the latest research in the field from around the globe.
Author: Leslie S. Emery
Publisher:
ISBN:
Category :
Languages : en
Pages : 162
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Book Description
The advent of large-scale population genomic datasets has enabled detailed inferences regarding human evolutionary history. Demographic changes and positive selection have left their marks on the genome and we can now begin to decipher them. In this dissertation, I present the work I have completed on the topic of human population genomic inference. In chapter 1, I begin by reviewing the importance of human genetic variation and the factors that influence it, focusing on the effects of demographic changes and positive selection. Chapter 2 describes an analysis of genetic ancestry in a worldwide sample of human populations. I show that mitochondrial lineage tests overlook large amounts of variation in genetic ancestry. In chapter 3, I focus on inferences regarding the effective sex ratio in the recent evolutionary past. I present a reanalysis of SNP and resequencing data that resolves a set of conflicting results from previous studies. Using coalescent simulations, I present a model of a recent male bias in effective population size, coupled with an earlier female bias, which is consistent with existing genetic variation on the X chromosome and the autosomes. In chapter 4, I present a comprehensive study of the performance of a battery of neutrality test statistics under a wide range of realistic models of positive selection in recent human evolution. I demonstrate that existing tests perform better than expected for detecting the signatures of a soft sweep from standing variation. Then, I develop a genome-wide approach, the Cumulative Selection Score (CSS), for combining the signals from multiple neutrality test statistics to detect the signatures of positive selection with greater accuracy. By implementing this approach in genomic variation data for chromosome 2, I show that the CSS can be applied to whole-genome datasets. I conclude in chapter 5 by discussing the potential of population genomic inferences and the future of the field.
Author: Julie Marie Granka
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
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.
Author: Daniel L. Hartl
Publisher: Sinauer Associates, Incorporated
ISBN:
Category : Science
Languages : en
Pages : 712
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Book Description
Darwinian evolution in mendelian populations. Random genetic drift. Mutation and the neutral theory. Natural selection. Inbreeding and other forms of nonrandom mating. Population subdivision and migration. Molecular population genetics. Evolutionary genetics of quantitative characters. Ecological genetics and speciation.
Author: Alexander G. Shanku
Publisher:
ISBN:
Category : Evolution (Biology)
Languages : en
Pages : 244
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Book Description
Historically, much of the research in evolutionary biology and population genetics has involved analysis at the level of either a single locus or a few number thereof. However, Next Generation sequencing technology has opened the floodgates with respect to both the sheer volume and quality of sequence data that researchers have long needed to address and answer long-standing questions in their fields. Scientists are now, by and large, no longer hampered in their efforts by technological hurdles to obtain data, but are in fact facing the problem of how best to use the vast amount of data that are accumulating at an ever-increasing rate. This is a good problem to have. The following research described in this dissertation is an attempt to derive answers to questions in the fields of population genetics and evolutionary biology that, until recently, have been either intractable or, at best, extremely difficult to address. In the first chapter I provide an introduction and a brief historical look at the research efforts that have proceeded my own. In the second chapter I describe how modern sequencing methods and computational analysis can be used to study, analyze, and answer evolutionary questions about the non-model organism, Enallagma hageni, in order to 1) determine this organism's phylogenetic position within Arthropoda, 2) provide answers and insight into the evolutionary history of the protein-encoding genes in the Enallagma transcriptome, and 3) give functional annotation to these expressed proteins. In the third chapter I examine how natural selection acts on the genome and derive a method that can accurately determine the evolutionary cause of nucleotide fixations, having occurred either through positive selection or neutral processes. I then apply the methodology to North American populations of Drosophila melanogaster, providing further evidence as to how adaptive evolution proceeds in a newly established population. This is an important question, for though there have been multiple approaches devised to determine the targets and modes of evolution in the genome, to date there has not emerged a definitive method which can determine both the location and type of a selective process, and as a result, the picture of how and where adaptive evolution proceeds in the genome has remained opaque. In the forth chapter I examine how levels of natural selection within the genome have the potential to inhibit the ability to accurately learn population demographic history. Using a number of modern algorithms and extensive simulations, I first examine whether or not demographic histories that are learned under simple biological assumptions will yield accurate results when the actual data itself does not adhere to these assumptions. Further, I go on to examine more complicated models of demographic history, looking specifically at how positive selection biases inference, which directions these biases occur, and at what levels of selection do inference methods fail to be robust. Finally, I describe potential evolutionary scenarios where these inference methods may be more prone to fail, as well as methods which might mitigate positive selection's effects, thus allowing for more accurate histories to be inferred. The work contained in this dissertation, at the broadest scale, is an effort to marry state-of-the-art techniques in statistics, computer science, and machine learning algorithms to the technological advances of next generation sequencing; the potent combination of these technologies has provided a means with which to derive answers to multiple, long-standing questions in population genetics and evolutionary biology.
Author: Dinesh Adhikary
Publisher: Springer Nature
ISBN: 3030723658
Category : Science
Languages : en
Pages : 181
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Book Description
This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.
