Lineages of the cyanobacteria Prochlorococcus marinus have diverged
into two genetically distinct ‘ecotypes,’ high-light adapted (HL) and low-light
adapted (LL), which thrive under different environmental conditions. This type
of niche differentiation in prokaryotes is often accompanied by genetic and
genomic divergence. Differential selection pressure associated with ecotype
divergence can be analyzed using models of codon evolution. However, some
characteristics of the Prochlorococcus genome violate underlying assumptions of
these models. For example, high levels of recombination between bacterial
strains are known to cause false positives for codon models. Therefore, it is
important that statistical methods for detecting recombination be reliable. In
Chapter 2, I evaluate a set of recombination detection methods under four
different scenarios related to functional divergence: 1) varying tree shape, 2)
positive selection, 3) non-stationary evolution, and 4) varying levels of
recombination and divergence.
| Identifer | oai:union.ndltd.org:LACETR/oai:collectionscanada.gc.ca:NSHD.ca#10222/13021 |
| Date | 17 August 2010 |
| Creators | Bay, Rachael |
| Source Sets | Library and Archives Canada ETDs Repository / Centre d'archives des thèses électroniques de Bibliothèque et Archives Canada |
| Language | English |
| Detected Language | English |
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