Neutral evolution of ten types of mariner transposons in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae

Ten types of mariner transposable elements (232 individual sequences) are present in the completed genomic DNA sequence of Caenorhabditis elegans and the partial sequence of Caenorhabditis briggsae. We analyze these replicated instances of mariner evolution and find that elements of a type have evolved within their genomes under no selection on their transposase genes. Seven of the ten reconstructed ancestral mariners carry defective transposase genes. Selection has acted during the divergence of some ancestral elements. The neutrally-evolving mariners are used to analyze the pattern of molecular evolution in Caenorhabditis. There is a significant mutational bias against transversions and significant variation in rates of change across sites. Deletions accumulate at a rate of 0.034 events/bp per substitution/site, with an average size of 166 bp (173 gaps observed). Deletions appear to obliterate preexisting deletions over time, creating larger gaps. Insertions accumulate at a rate of 0.019 events/bp per substitution/site, with an average size of 151 bp (61 events). Although the rate of deletion is lower than most estimates in other species, the large size of deletions causes rapid elimination of neutral DNA: a mariner's "half-life" (the time by which half an element's sequence should have been deleted) is ∼0.1 subsitutions/site. This high rate of DNA deletion may explain the compact nature of the nematode genome.