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 Bacterial Population Genetics in Infectious Disease eBook

Bacterial Population Genetics in Infectious Disease


eBook Publisher: John Wiley & Sons
Imprint: Wiley-Blackwell

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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

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Title of eBook: Bacterial Population Genetics in Infectious Disease
Release Date: 03-16-2010
Publisher: Wiley-Blackwell

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Parent title Bacterial Population Genetics in...
Encrypted (DRM) Yes
SKU 9780470600115
File size 9064
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Bacterial Population Genetics in Infectious Disease


Chapter One

The Coalescent of Bacterial Populations

Mikkel H. Schierup and Carsten Wiuf

1.1 BACKGROUND AND MOTIVATION

Recent years have seen an explosion in the number of available DNA sequences from many different species. Whereas small genomic regions routinely have been sequenced for more than 20 years and have improved our knowledge of genetic variation at the species and the population levels, new high-throughput techniques have made possible the sequencing of whole genomes and genomic regions for many individuals at an affordable price and in a realistic time frame. This offers unprecedented opportunities for studying genetic variation within and between species and the effects of variation on transcription, regulation, and expression. So, for example, population data sets for bacteria are now expected to consist of full genomes rather than single genes, and the limitations to evolutionary inference are more likely to be found in the analysis rather than in the generation of sequence data (see Chapter 7 of this book).

In the following, we will discuss a mathematical model-the coalescent-that describes the process of generating genetic data, with special reference to bacterial populations. For simplicity, we assume the data are in the form of DNA sequences; however, other forms of genetic markers can likewise be modeled. The sequences (or genes) are all homologous copies of the same genetic region in the genome of a species. The relevance of such a model becomes clear when we want to infer/learn details about the evolutionary processes that generated and shaped a sample of present-day sequences. This process m

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