Patterns and rates of indel evolution in processed pseudogenes from humans and murids

Patterns and rates of indel (deletions and insertions) evolution were characterized in 156 independently derived processed pseudogenes from humans and murids (mice and rats). A total of 441 deletions and 161 insertions were unambiguously identified. On a subset of 109 pseudogenes, we verified and confirmed the assumption that indels occur almost exclusively in the pseudogene and, therefore, in comparisons between pseudogenes and their functional paralogs, it is possible to assign polarity to the indel event. By comparing the characteristics of terminal truncations with those of internal deletions, we find support for the hypothesis that truncations are generated through a different pathway than internal deletions. The number of deletions and insertions per pseudogene was found to increase monotonically with time. Deletions occur on average once every 40 nucleotide substitutions, whereas insertions are much rarer, occurring once every 100 substitutions, indicating that the mechanisms involved in deletion formation are most probably different from those responsible for the formation of insertions. The age of the pseudogene, however, explained only 20 and 13%, respectively, of the variation in the number of deletions and insertions per site, indicating that factors other than evolutionary time may play a significant role in the evolutionary dynamics of indel accumulation. Since the rate of substitution has been previously shown to be higher in murids than in humans, we deduce that deletions and insertions accumulate proportionally faster in murids than in humans. Deletions and insertions in murid and human genomes do not contribute significantly to genome size.