The origins of eukaryotic gene structure

Research output: Contribution to journalArticlepeer-review

280 Scopus citations


Most of the phenotypic diversity that we perceive in the natural world is directly attributable to the peculiar structure of the eukaryotic gene, which harbors numerous embellishments relative to the situation in prokaryotes. The most profound changes include introns that must be spliced out of precursor mRNAs, transcribed but untranslated leader and trailer sequences (untranslated regions), modular regulatory elements that drive patterns of gene expression, and expansive intergenic regions that harbor additional diffuse control mechanisms. Explaining the origins of these features is difficult because they each impose an intrinsic disadvantage by increasing the genic mutation rate to defective alleles. To address these issues, a general hypothesis for the emergence of eukaryotic gene structure is provided here. Extensive information on absolute population sizes, recombination rates, and mutation rates strongly supports the view that eukaryotes have reduced genetic effective population sizes relative to prokaryotes, with especially extreme reductions being the rule in multicellular lineages. The resultant increase in the power of random genetic drift appears to be sufficient to overwhelm the weak mutational disadvantages associated with most novel aspects of the eukaryotic gene, supporting the idea that most such changes are simple outcomes of semi-neutral processes rather than direct products of natural selection. However, by establishing an essentially permanent change in the population-genetic environment permissive to the genome-wide repatterning of gene structure, the eukaryotic condition also promoted a reliable resource from which natural selection could secondarily build novel forms of organismal complexity. Under this hypothesis, arguments based on molecular, cellular, and/or physiological constraints are insufficient to explain the disparities in gene, genomic, and phenotypic complexity between prokaryotes and eukaryotes.

Original languageEnglish (US)
Pages (from-to)450-468
Number of pages19
JournalMolecular biology and evolution
Issue number2
StatePublished - Feb 2006
Externally publishedYes


  • Complexity
  • Gene networks
  • Gene regulation
  • Gene structure
  • Genetic draft
  • Genome evolution
  • Introns
  • Modularity
  • Mutation
  • Natural selection
  • Pleiotropy
  • Population size
  • Random genetic drift
  • Recombination
  • Subfunctionalization
  • Transcription factors
  • UTR

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


Dive into the research topics of 'The origins of eukaryotic gene structure'. Together they form a unique fingerprint.

Cite this