1 Academy of Ecology, Marine Biology and Biotechnology,
Far Eastern National University 690600 Vladivostok,
Oktyabrskaya St., 27, Tell Fax: 7-(4232)-2595409
Institute of Marine Biology ofRAS
e-mail: esbalak@bio.dvgu.ru
690041 Far East Branch, Vladivostok, Palchevsky St., 17
2University of California,
Department of Ecology and Evolutionary Biology,
92697-2525, Irvine, С A, USA
e-mail: fjayala@uci.edu
Pseudogenes have been defined as nonfunctional sequences of genomic DNA (junk DNA) originally derived from functional genes. It is therefore assumed that pseudogenes are not subject to natural selection and consequently pseudogene mutations are selectively neutral and have equal probability to become fixed in the population. We describe some unexpected features of pseudogenes in diverse organisms that are inconsistent with this widely accepted point of view. Pseudogenes are often evolutionary conserved and transcriptionally active. Moreover, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene regulation, generation of genetic diversity, and other features that are expected in genes or DNA sequences that have functional roles. A review of the evidence leads to the conclusion that pseudogenes are important components of genomes, representing a repertoire of sequences available for functional evolution and subject to non-neutral evolutionary changes. Pseudogenes might be considered as potogenes, i.e. DNA sequences with a potentiality for becoming new genes or acquire new functions. Furthermore we conjecture that some pseudogenes along with their parental sequences may constitute sets of indivisible functionally interacting entities (intergenic complexes or "intergenes"), in which all the component elements are required in order to fulfill a collective functional role.
