By D. Ashley Robinson, Edward J Feil, Daniel Falush
This booklet is a distinct synthesis of the most important recommendations and techniques in bacterial inhabitants genetics in infectious affliction, a box that's now approximately 35 yrs old. Emphasis is given to explaining population-level methods that form genetic edition in bacterial populations and statistical equipment of study of bacterial genetic facts. A "how to" of bacterial inhabitants genetics, which covers an exceptionally huge diversity of organismsExpanding quarter of technology because of high-throughput genome sequencing of bacterial pathogensCovers either basic ways to examining bacterial inhabitants constructions with conceptual historical past in bacterial inhabitants biologyDetailed therapy of statistical equipment
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Additional resources for Bacterial Population Genetics in Infectious Disease
2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319, 1100–1104. , Yamaoka, Y. et al. (2009) The peopling of the Pacific from a bacterial perspective. Science 323, 527–530. Sniegowski, P. (2004) Evolution: Bacterial mutation in stationary phase. Curr Biol 14, R245–R246. Tajima, F. (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437–460. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
While the use of the word clonal in this context broadly implies very modest rates of recombination, the term is also used for highly uniform species, such as Bacillus anthracis, where all isolates appear identical by MLEE/MLST. As recombination between identical sequences will not leave any genetic footprint, so it is not possible to reliably gauge how much recombination occurs within such populations, only that DNA does not appear to be imported from elsewhere. “Clonal complex” is a related term, and this will be discussed at more length elsewhere in the chapter.
And Hein, J. (2000) The coalescent with gene conversion. Genetics 155, 451–462. Wright, S. (1931) Evolution in Mendelian populations. Genetics 16, 97–159. Chapter 2 Linkage, Selection, and the Clonal Complex Edward J. 1 INTRODUCTION—HISTORICAL OVERVIEW There are two reasons one may wish to distinguish one bacterial strain from another. The first is that assaying genetic variation within natural populations is a prerequisite to addressing key evolutionary questions such as the molecular processes underlying the emergence of variation (mutation and recombination) or the processes (selection and drift) that determine the subsequent fate of this variation.