| Summary: | Caenorhabditis elegans is arguably the best understood animal on the planet.
Used for over 50 years to study development, we have a vast amount of knowledge of
the inner workings of this worm. Our knowledge is incomplete, however, without
placing this organism in its evolutionary and ecological context. In this body of work,
I focused on examining the evolutionary forces shaping Caenorhabditis nematodes,
with a particular emphasis on C. briggsae. In the first part, I examined the evolution
of mitochondrial genomes throughout the genus. I tested for signatures of selection
and examined the evolution of mitochondrial genome architecture. Through this, I
have shown that the mitochondrial genomes of Caenorhabditis nematodes appear to
be primarily influenced by purifying selection and that molecular evolutionary
inference is greatly limited by mutational saturation. The evolutionary forces acting
on mitochondrial genomes have been examined before, however, this study,
extensively examining this within a single genus, provides a much better
characterization than any of the studies to date. In the second part, I characterized the
evolutionary dynamics of mitochondrial pseudogenes in C. briggsae and its closest
relatives. I showed that these elements, while they might not evolve under strictly
neutral terms, are still quite useful in uncovering cryptic diversity and population
structure. I also observed that they appear/disappear in a manner that appears
inconsistent with one commonly held model for mitochondrial pseudogene evolution.
In the final part, I examined the evolution of C. briggsae in response to a biotic
environment. I showed that fitness in a parasite-containing environment incurs a
trade-off with fitness in the absence of parasites. Together, the chapters of this
dissertation demonstrate the strength of Caenorhabditis, and in particular C. briggsae,
for examining evolutionary questions and advances this system as a tool for
evolutionary biology research. === Graduation date: 2013
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