Evolution of Germline-Limited Sequences in Two Populations of the Ciliate Chilodonella uncinata

Ciliates are microbial eukaryotes that separate their nuclear functions into a germline micronucleus and a somatic macronucleus. During development of the macronucleus the genome undergoes a series of reorganization events that includes the precise excision of intervening DNA. Here, we determine the architecture of four loci in the micronuclear and macronuclear genomes of the ciliate and compare the levels of variation in micronuclear-limited sequences to macronuclear destined sequences at two of these loci. We find that within a population, germline-limited sequences are evolving at the same rate as other putatively neutral sites, but between populations germline-limited sequences are accumulating mutations at a much faster rate than other sites. We also find evidence of macronuclear recombination and incomplete elimination of intervening DNA, which result in increased diversity in the macronuclear genome. Our results support the assertion that the unusual genomic features of ciliates can result in rapid and unpredicted patterns of diversification.