BTW, you said “most”. My criticism was of “most”, not the process. Until the entire genome has been examined in every particular I don’t think you can say “most”.
There have been a few pseudogenes that have been assigned putative function based upon their evolutionary conservation. This was because they DID do a genome wide survey of pseudogenes and saw a few that stood out against the background because these lucky few WERE evolutionarily conserved. What they might do, or why they show conservation has yet to be determined; but the fact is that MOST pseudogenes change at the neutral mutation rate because they do not perform a function and so are ‘neutral’ to selective pressure.
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates.Khelifi A, Meunier J, Duret L, Mouchiroud D.
Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Claude Bernard-Lyon 1, 16 rue Raphael Dubois, 69622 Villeurbanne Cedex, France. khelifi@biomserv.univ-lyon1.fr
Processed pseudogenes are generated by reverse transcription of a functional gene. They are generally nonfunctional after their insertion and, as a consequence, are no longer subjected to the selective constraints associated with functional genes. Because of this property they can be used as neutral markers in molecular evolution. In this work, we investigated the relationship between the evolution of GC content in recently inserted processed pseudogenes and the local recombination pattern in two mammalian genomes (human and mouse). We confirmed, using original markers, that recombination drives GC content in the human genome and we demonstrated that this is also true for the mouse genome despite lower recombination rates. Finally, we discussed the consequences on isochores evolution and the contrast between the human and the mouse pattern.
PMID: 16752212 [PubMed - indexed for MEDLINE]