Genome-Level Analysis of Selective Constraint without Apparent Sequence Conservation

Conservation of function can be accompanied by obvious similarity of homologous sequences which may persist for billions of years (Iyer LM, Leipe DD, Koonin EV, Aravind L. 2004. Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 146:11-31.). However, presumably homologous segments of noncoding DNA can also retain their ancestral function even after their sequences diverge beyond recognition (Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS. 2006. Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312:276-279.). To investigate this phenomenon at the genomic scale, we studied homologous introns in a quartet of insect species, and in a quartet of vertebrate species. Each quartet consisted of two pairs of moderately distant genomes, with a much larger evolutionary distance between the pairs. In both quartets, we found that introns that carry a regulatory segment or a conserved segment in the first pair tend to carry a conserved segment in the second pair, even though no similarity of these segments could be detected between the two pairs. Furthermore, introns from one pair that are preserved in the other pair tend to carry a conserved segment within the first pair, and be longer in the first pair, compared with the introns that were lost between pairs, even though no similarity between pairs could be detected in such preserved introns. These results indicate that selective constraint, presumably caused by conservation of the ancestral function, often persists even after the homologous DNA segments become unalignable.