Caenorhabditis elegans is one of the preeminent model organisms in modern biology, but only recently have we started to understand the details of its natural ecology and evolutionary history. Studying C. elegans alongside its closest relatives provides an important evolutionary context for the origins and constraints that have resulted in the particular instance analyzed in the laboratory. A focussed search for new Caenorhabditis species over the last decade has led to the discovery of over 50 species of Caenorhabditis. As part of an international collaboration, the Caenorhabditis Genomes Project (CGP), we have sequenced the genomes of all Caenorhabditis species currently in culture. We exploit these new genome sequences to perform the most comprehensive reconstruction of the Caenorhabditis phylogeny to date, providing an essential evolutionary framework for downstream analyses. We reveal extensive variation in genome size in the genus, ranging from the 48 Mb genome of C. drosophilae to the 160 Mb genome of C. vivipara. Investigating the origins of this variation, we find that protein-coding gene number is highly correlated with genome size, with C. drosophilae possessing just 13,000 genes due to extensive gene loss. Other genomic features, such as repeat (mobile element) proliferation also contribute to genome size changes. Among the non-coding portions of these genomes, we identified rapid and extensive intron loss across the genus, including in the group that includes C. elegans. We demonstrate the utility of these genome sequences for C. elegans research by analyzing the evolutionary history of key signaling pathways, revealing unexpected complexity. We have made these genomic resources, including genus-wide orthology sets, publicly available via the CGP website
(http://www.caenorhabditis.org) which includes a dedicated genome browser and a BLAST server. These new species and their associated genomic resources add to the arsenal of tools available to the C. elegans researcher to interrogate biology of this important nematode. The CGP is a collaboration between the following labs: Blaxter (Edinburgh), Felix (Paris), Ailion (Washington), Andersen (Northwestern), Braendle (Nice), Cutter (Toronto), Fitch (NYU), Fierst (Alabama), Kikuchi (Miyazaki), Rockman (NYU), Schwarz (Cornell), Wang (Academia Sinica).