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Evolutionary Theory and Processes: Modern Horizons pp 177–193Cite as

Pseudogenes are Not Junk DNA

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Abstract

We describe some unexpected features of pseudogenes in diverse organisms that are inconsistent with the traditional view that considers pseudogenes as nonfunctional sequences of genomic DNA (“junk” DNA) not subject to natural selection. Pseudogenes are often evolutionarily conserved and transcriptionally active. Moreover, there is evidence indicating that some pseudogenes engage in regulation of gene expression and generation of genetic diversity. Pseudogene patterns of nucleotide variability evince that not all pseudogene mutations are selectively neutral and, thus, do not all have equal probability of becoming fixed in the population. A pseudogene that has arisen by duplication or retroposition may, at first, not be subject to natural selection, if the source gene remains functional. Therefore, alleles of the pseudogene will accumulate mutations, including disabling mutations, over time. But a mutant allele that incorporates a new function may be favored by natural selection and will have enhanced probability of becoming fixed in the population. Thus, some pseudogenes that have lost the original function may have acquired new ones. 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 (following the terminology of J. Brosius and S.J. Gould, 1992), i.e., DNA sequences with a potentiality for becoming new genes (Balakirev and Ayala, 2003). 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.

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Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697-2525, USA

    Evgeniy S. Balakirev & Francisco J. Ayala

  2. Institute of Marine Biology, Vladivostok, 690041, Russia

    Evgeniy S. Balakirev

  3. Academy of Ecology, Marine Biology, and Biotechnology, Far Eastern State University, Vladivostok, 690600, Russia

    Evgeniy S. Balakirev

Authors
  1. Evgeniy S. Balakirev
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  2. Francisco J. Ayala
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Editors and Affiliations

  1. Institute of Evolution, University of Haifa, Haifa, Israel

    Solomon P. Wasser

  2. N.G. Kholodny Institute of Botany, NASU, Kiev, Ukraine

    Solomon P. Wasser

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© 2004 Springer Science+Business Media Dordrecht

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Balakirev, E.S., Ayala, F.J. (2004). Pseudogenes are Not Junk DNA. In: Wasser, S.P. (eds) Evolutionary Theory and Processes: Modern Horizons. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-0443-4_10

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  • DOI: https://doi.org/10.1007/978-94-017-0443-4_10

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-90-481-6457-8

  • Online ISBN: 978-94-017-0443-4

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