Pseudogene evolution and natural selection for a compact genome

Pseudogenes are nonfunctional copies of protein-coding genes that are presu med to evolve without selective constraints on their coding function. They are of considerable utility in evolutionary genetics because, in the absenc e of selection, different types of mutations in pseudogenes should have equ al probabilities of fixation. This theoretical inference justifies the esti mation of patterns of spontaneous mutation from the analysis of patterns of substitutions in pseudogenes, Although it is possible to test whether pseu dogene sequences evolve without constraints for their protein-coding functi on, it is much more difficult to ascertain whether pseudogenes may affect f itness in ways unrelated to their nucleotide sequence. Consider the possibi lity that a pseudogene affects fitness merely by increasing genome size. If a larger genome is deleterious-for example, because of increased energetic costs associated with genome replication and maintenance-then deletions, w hich decrease the length of a pseudogene, should be selectively advantageou s relative to insertions or nucleotide substitutions. In this article we ex amine the implications of selection for genome size relative to small (1-40 0 bp) deletions, in light of empirical evidence pertaining to the size dist ribution of deletions observed in Drosophila and mammalian pseudogenes, The re is a large difference in the deletion spectra between these organisms. W e argue that this difference cannot easily be attributed to selection for o verall genome size, since the magnitude of selection is unlikely to be stro ng enough to significantly affect the probability of fixation of small dele tions in Drosophila.