What can deep sequencing reveal about bacterial evolution? Diversity and dynamics in a biofilm
- This thesis explores the genetic variability of Synechococcus cyanobacteria found in a Yellowstone National Park hot spring with the aim of better understanding the evolutionary and ecological processes that give rise to bacterial diversity. The primary data used was deep, amplicon sequencing reads, and as these contain numerous sources of errors, the first chapter introduces an error model and a novel error correction algorithm. Using this algorithm, the second chapter describes statistical features of the diversity that suggest that this population is quasi-sexual — having a high rate of homologous recombination. The final chapter examines the diversity in greater detail, finding many puzzles and contradictory results, and ultimately concluding that this population reveals dynamics too rich -- a mixture of recombination, hitchhiking, deleterious mutations, epistasis, and dispersal in a meta-population -- to be adequately modeled by current population genetic theory.
|Type of resource
|electronic; electronic resource; remote
|1 online resource.
|Rosen, Michael Jeremy
|Stanford University, Department of Applied Physics.
|Statement of responsibility
|Michael Jeremy Rosen.
|Submitted to the Department of Applied Physics.
|Thesis (Ph.D.)--Stanford University, 2016.
- © 2016 by Michael Jeremy Rosen
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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