Population Dynamics and Population Genetics of RecombinationinBacteria Pubblico
Cornejo, Omar (2009)
Abstract
Although a rare event and unnecessary for reproduction, for many species of bacteria, recombination broadly defined to include the acquisition of genes from other, at times very divergent, organisms plays a fundamental role as a source of variation for adaptive evolution. What about more mundane horizontal gene transfer (HGT) events: homologous gene recombination (HGR) among members of the same population? While there no question about central role of HGR has played as tool for understanding the genetics and molecular biology of bacteria, the role of this kind of gene shuffling for the evolution of bacteria is not at all clear. The motivation for the research in this dissertation was to increase our understanding of the contribution of HGR to adaptive evolution in bacteria, reviewed in the background Chapter 1. And, save for serendipitous observation, the profound toxin-mediated oscillations in the densities of Streptococcus pneumoniae in continuous culture described in Chapter 2, the population and evolutionary dynamics of HGR in bacteria is the focus of this dissertation. The third chapter explores the factors that constrain the extent to which different strains of S. pneumoniae engage in shuffling their genes by HGR. The fourth chapter, we use a semi-stochastic simulation of mutation, selection and recombination to ascertain the conditions under which, and extent to which, HGR accelerates the rate at which bacterial populations adapt to their environment. More importantly, we assess the conditions under which the capacity to increase rates of adaptive evolution will select for the evolution and maintenance of mechanisms for HGR while competing recombining vs non-recombining populations.
Table of Contents
1. CHAPTER 1. INTRODUCTION 1 1.1 Some of the background behind 5 1.2 Population dynamics of Streptococcus pneumoniae 10 1.3 Population Genetic Structure in Streptococcus pneumoniae 12 1.4 Evolutionary dynamics of recombination in bacteria 14 2. CHAPTER 2. OSCILLATIONS IN CONTINUOUS CULTURE POPULATIONS OF STREPTOCOCCUS PNEUMONIAE: POPULATION DYNAMICS AND THE EVOLUTION OF CLONAL SUICIDE 18 2.1 Introduction 18 2.2 Materials and Methods 21 2.2.1 Bacteria 21 2.2.2 Culture media 23 2.2.3 Chemostat Culture and Sampling 23 2.2.4 Bio-Assay for Toxin 24 2.2.5 Recombination Assay 25 2.2.6 Invasion Experiments 26 2.2.6 Numerical Analysis (Simulations) 27 2.3 Results 27 2.4 Discussion and Conclusions 43 3. CHAPTER 3. POLYMORPHIC COMPETENCE PEPTIDE DOES NOT LIMIT RECOMBINATION IN STREPTOCOCCUS PNEUMONIAE 51 3.1 Introduction 51 3.2 Materials and Methods 54 3.2.1 Clinical Isolates of S. pneumoniae 54 3.2.2 Genetic Characterization 54 3.2.3 Population Genetic Analyses 56 3.3 Results 60 3.4 Discussion and Conclusions 68 4. CHAPTER 4. THE POPULATION AND EVOLUTIONARY DYNAMICS OF HOMOLOGOUS GENE RECOMBINATION IN BACTERIAL
POPULATIONS 74 4.1 Introduction 74 4.2 Methods 77 4.3 Results 83 4.4 Discussion and Conclusions 95 5 CHAPTER 5. SUMMARY AND OUTLOOK 108 6 BIBLIOGRAPHY 112 7 APPENDIX 122 7.1 Supplementary Information: Oscillatory dynamics in S. pneumoniae 123 7.2 Supplementary Information: Population Structure S. pneumoniae 138
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