Bacterial Population Genetics in Infectious Disease

Informationen zum Autor D. Ashley Robinson is an Associate Professor of Microbiology at The University of Mississippi Medical Center. Her specialties include bacterial genetics, microbial evolution and antimicrobial resistance, among others. Daniel Falush is a Research Fellow in the Department of Statistics at the University of Oxford, where he specializes in mathematical biology, particularly mathematical genetics and bioinformatics. Edward Feil is a Reader in Microbial Evolution at University of Bath. He studies bacterial evolution and genetic recombination as well as the biogeography of pathogenic bacteria. Klappentext This book is a unique synthesis of the major concepts and methods in bacterial population genetics in infectious disease, a field that is now about 35 yrs old. Emphasis is given to explaining population-level processes that shape genetic variation in bacterial populations and statistical methods of analysis of bacterial genetic data. A "how to" of bacterial population genetics, which covers an extremely large range of organisms Expanding area of science due to high-throughput genome sequencing of bacterial pathogens Covers both fundamental approaches to analyzing bacterial population structures with conceptual background in bacterial population biology Detailed treatment of statistical methods Zusammenfassung This book is a unique synthesis of the major concepts and methods in bacterial population genetics in infectious disease, a field that is now about 35 yrs old. Emphasis is given to explaining population-level processes that shape genetic variation in bacterial populations and statistical methods of analysis of bacterial genetic data. Inhaltsverzeichnis Foreword.Preface.Contributors.Part I Concepts and Methods in Bacterial Population Genetics.1 The Coalescent of Bacterial Populations.1.1 Background and Motivation.1.2 Population Reproduction Models.1.3 Time and the Effective Population Size.1.4 The Genealogy of a Sample of Size n.1.5 From Coalescent Time to Real Time.1.6 Mutations.1.7 Demography.1.8 Recombination and Gene Conversion.1.9 Summary.2 Linkage, Selection, and the Clonal Complex.2.1 Introduction--Historical Overview.2.2 Recombination, Linkage, and Substructure.2.3 Neutrality versus Selection.2.4 Clustering Techniques.3 Sequence-Based Analysis of Bacterial Population Structures.3.1 Introduction.3.2 Alignments.3.3 Phylogenetic Methods.3.4 Measures of Uncertainty.3.5 Beyond the Tree Model.4 Genetic Recombination and Bacterial Population Structure.4.1 Introduction.4.2 Constraints on LGT.4.3 Infl uences of LGT on Sequence Analyses.4.4 The Detection of Individual LGT Events.4.5 The Estimation of Homologous Recombination Rates.4.6 Properly Accounting for LGT During Sequence Analyses.4.7 Questions Relating Directly to LGT.5 Statistical Methods for Detecting the Presence of Natural Selection in Bacterial Populations.5.1 Introduction.5.2 Natural Selection.5.3 Statistical Methods for Detecting the Presence of Natural Selection.5.4 Statistical Methods for Bacterial Populations.5.5 An Example.5.6 Discussion and Perspective.6 Demographic Infl uences on Bacterial Population Structure.6.1 Bacterial Population Size.6.2 Measures of Genetic Diversity.6.3 The Concept of Effective Population Size.6.4 Inferring Past Demography from Genetic Sequence Data.6.5 Population Subdivision.6.6 What is a Bacterial Population?6.7 Conclusion.7 Population Genomics of Bacteria.7.1 Introduction.7.2 Classical Bacterial Population Genetics.7.3 The Genomics Era.7.4 Bacterial Population Genomics.7.5 Next-Gen Bacterial Population Genomics.7.6 Next-Gen Genomics Technology.7.7 Next-Gen Genomic Data Analysis.7.8 Conclusions/Future Prospects.8 The Use of MLVA and SNP Analysis to Study the Population Genetics of Pathogenic Bacteria.8.1 Introducti...

Autorentext
D. Ashley Robinson is an Associate Professor of Microbiology at The University of Mississippi Medical Center. Her specialties include bacterial genetics, microbial evolution and antimicrobial resistance, among others. Daniel Falush is a Research Fellow in the Department of Statistics at the University of Oxford, where he specializes in mathematical biology, particularly mathematical genetics and bioinformatics. Edward Feil is a Reader in Microbial Evolution at University of Bath. He studies bacterial evolution and genetic recombination as well as the biogeography of pathogenic bacteria.

Klappentext

This book is a unique synthesis of the major concepts and methods in bacterial population genetics in infectious disease, a field that is now about 35 yrs old. Emphasis is given to explaining population-level processes that shape genetic variation in bacterial populations and statistical methods of analysis of bacterial genetic data. A "how to" of bacterial population genetics, which covers an extremely large range of organisms Expanding area of science due to high-throughput genome sequencing of bacterial pathogens Covers both fundamental approaches to analyzing bacterial population structures with conceptual background in bacterial population biology Detailed treatment of statistical methods

Inhalt
Foreword. Preface. Contributors. Part I Concepts and Methods in Bacterial Population Genetics. 1 The Coalescent of Bacterial Populations. 1.1 Background and Motivation. 1.2 Population Reproduction Models. 1.3 Time and the Effective Population Size. 1.4 The Genealogy of a Sample of Size n. 1.5 From Coalescent Time to Real Time. 1.6 Mutations. 1.7 Demography. 1.8 Recombination and Gene Conversion. 1.9 Summary. 2 Linkage, Selection, and the Clonal Complex. 2.1 Introduction--Historical Overview. 2.2 Recombination, Linkage, and Substructure. 2.3 Neutrality versus Selection. 2.4 Clustering Techniques. 3 Sequence-Based Analysis of Bacterial Population Structures. 3.1 Introduction. 3.2 Alignments. 3.3 Phylogenetic Methods. 3.4 Measures of Uncertainty. 3.5 Beyond the Tree Model. 4 Genetic Recombination and Bacterial Population Structure. 4.1 Introduction. 4.2 Constraints on LGT. 4.3 Infl uences of LGT on Sequence Analyses. 4.4 The Detection of Individual LGT Events. 4.5 The Estimation of Homologous Recombination Rates. 4.6 Properly Accounting for LGT During Sequence Analyses. 4.7 Questions Relating Directly to LGT. 5 Statistical Methods for Detecting the Presence of Natural Selection in Bacterial Populations. 5.1 Introduction. 5.2 Natural Selection. 5.3 Statistical Methods for Detecting the Presence of Natural Selection. 5.4 Statistical Methods for Bacterial Populations. 5.5 An Example. 5.6 Discussion and Perspective. 6 Demographic Infl uences on Bacterial Population Structure. 6.1 Bacterial Population Size. 6.2 Measures of Genetic Diversity. 6.3 The Concept of Effective Population Size. 6.4 Inferring Past Demography from Genetic Sequence Data. 6.5 Population Subdivision. 6.6 What is a Bacterial Population? 6.7 Conclusion. 7 Population Genomics of Bacteria. 7.1 Introduction. 7.2 Classical Bacterial Population Genetics. 7.3 The Genomics Era. 7.4 Bacterial Population Genomics. 7.5 Next-Gen Bacterial Population Genomics. 7.6 Next-Gen Genomics Technology. 7.7 Next-Gen Genomic Data Analysis. 7.8 Conclusions/Future Prospects. 8 The Use of MLVA and SNP Analysis to Study the Population Genetics of Pathogenic Bacteria. 8.1 Introduction. 8.2 MLVA and Other DNA Fragment-Based Methods. 8.3 SNP and DNA Sequence-Based Methods. 8.4 Conclusion. Part II Population Genetics of Select Bacterial Pathogens. 9 Population Genetics of Bacillus: Phylogeography of Anthrax in North America. 9.1 Introduction. 9.2 History of Anthrax in North America. 9.3 The Anthrax Districts after 1944. 9.4 Molecular Genotyping of B. anthracis. 9.5 Genotypes within the Anthrax Districts in North America. 9.6 Phylogenetic Resolution within the WNA Lineage. 9.7 Phylogeographic Resolution within the Ames Lineage. 9.8 Additional B. anthracis Genotypes in North America. 9.9 Conclusions. 10 Population Genetics of Campylobacter. …