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 in sertions were unambiguously identified. On a subset of 109 pseudogenes , we verified and confirmed the assumption that indels occur almost ex clusively in the pseudogene and, therefore, in comparisons between pse udogenes and their functional paralogs, it is possible to assign polar ity to the indel event. By comparing the characteristics of terminal t runcations with those of internal deletions, we find support for the h ypothesis that truncations are generated through a different pathway t han internal deletions. The number of deletions and insertions per pse udogene 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 th at the mechanisms involved in deletion formation are most probably dif ferent 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, i ndicating that factors other than evolutionary time may play a signifi cant role in the evolutionary dynamics of indel accumulation. Since th e rate of substitution has been previously shown to be higher in murid s than in humans, we deduce that deletions and insertions accumulate p roportionally faster in murids than in humans. Deletions and insertion s in murid and human genomes do not contribute significantly to genome size. (C) 1997 Elsevier Science B.V.