Genes in nematode and ascidian genomes frequently occur in operons--multiple 
genes sharing a common promoter to generate a polycistronic primary 
transcript--and such genes comprise 15-20% of the coding genome for 
Caenorhabditis elegans and Ciona intestinalis. Recent work in nematodes has 
demonstrated that the identity of genes within operons is highly conserved among 
species and that the unifying feature of genes within operons is that they are 
expressed in germline tissue. However, it is generally unknown what processes 
are responsible for generating the distribution of operon sizes across the 
genome, which are composed of up to eight genes per operon. Here we investigate 
several models for operon evolution to better understand their abundance, 
distribution of sizes, and evolutionary dynamics over time. We find that 
birth-death models of operon evolution reasonably describe the relative 
abundance of operons of different sizes in the C. elegans and Ciona genomes and 
generate predictions about the number of monocistronic, nonoperon genes that 
likely participate in the birth-death process. This theory, and applications to 
C. elegans and Ciona, motivates several new and testable hypotheses about 
eukaryote operon evolution.