Genome evolution in the genus Caenorhabditis
The free-living nematode Caenorhabditis elegans is an important laboratory model organism that has been fundamental to the understanding of metazoan biology. However, until recently, C. elegans has largely been studied in isolation, with its evolutionary history poorly understood. Recent progress in our understanding of natural ecology of C. elegans has led to the discovery of many new species from the genus Caenorhabditis, most of which are in laboratory culture. In 2014, an international collaboration was launched which aimed to sequence the genomes of all species currently in culture. In this thesis, I present draft genomes for 38 Caenorhabditis species generated using both short- and long-read technology. I also present the genome of C. bovis, a species which appears to live parasitically in the ears of cattle in Eastern Africa. I exploited these and other genome sequences to perform the most comprehensive reconstruction of the Caenorhabditis phylogeny to date. Analysing genome size and content within the context of this phylogeny, I reveal extensive variation in genome size that is driven by changes in gene number and repetitive content. The work presented in this thesis represents a substantial contribution to the understanding of genome evolution in Caenorhabditis. Moreover, these data will become fundamental in our attempts to understand the evolutionary origins of this important model organism.