Evolution of pseudogenes and its relevance to the neutrality vs selection controversy

A pseudogene is a DNA segment that shows high homology to a functional gene but contains nucleotide chanbes such as frameshift and nonsense mutations that prevent its expression. All pseudogenes seem to have been produced by nonfunctionalization of duplicated genes. We have developed a theory for estimating the time since divergence between a pseudogene and its functional counterpart, the time since nonfunctionalization of the pseudogene and its rate of nucleotide substitution. We have applied this theory to three pseudogenes in the globin gene families: mouse ψα3, human, ψα1 and rabbit φβ2. Our results are as follows: The mouse ψα3 diverged from the α1 gene about 27 million years (MY) ago and became a pseudogene about 5 MY later; the human ψα1 was duplicated from the α gene about 42 MY ago and became nonfunctional almost immediately; the rabbit ψβ2 also became nonfunctional almost immediately after its duplication from the β1 gene about 34 MY ago. The rates of nucleotide substitution per site per year are estimated to be 5.0 x 10^-9, 5.5 x 10^-9 and 4.3 x 10^-9 for these three pseudogenes, respectively. The average rate of 4.9 x 10^-9 is about two times the average rate at the third position of codons and about eight times the average rate at the first two positions of codons in the functional α and β globin genes. Since pseudogenes apparently do not have any function and the third position of codons in a functional gene is generally subject to weaker functional constraints than the first two positions, our results clearly indicate that functionally less important genes or parts of genes evolve faster than functionally more important ones. These results can easily be explained by the neutral mutation hypothesis but are imcompatible with the selectionists' view. Supported by grants from NSF and NIH.