Synonymous substitution rates in Drosophila: Mitochondrial versus nuclear genes

Etsuko N. Moriyama, Jeffrey R. Powell

Research output: Contribution to journalArticle

120 Citations (Scopus)

Abstract

Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3) only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using these methods, we found that mitochondrial genes have 1.7-3.4 times higher synonymous substitution rates than the fastest nuclear genes or 4.5-9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was 2.7 (estimated from the melanogaster species subgroup) or 2.9 (estimated from the obscura group) times higher in mitochondrial genes than in nuclear genes. Synonymous transversions in mitochondrial genes occurred at an approximately equivalent rate to those in the fastest nuclear genes. This last result is not consistent with the hypothesis that the difference in turnover rates between mitochondrial and nuclear genomes is the major factor determining higher synonymous substitution rates in mtDNA. We conclude that the difference in synonymous substitution rates is due to a combination of two factors: a higher transitional mutation rate in mtDNA and constraints on nuclear genes due to selection for codon usage.

Original languageEnglish (US)
Pages (from-to)378-391
Number of pages14
JournalJournal of Molecular Evolution
Volume45
Issue number4
DOIs
StatePublished - Oct 16 1997

Fingerprint

Mitochondrial Genes
Drosophila
substitution
Substitution reactions
Genes
gene
Base Composition
Mitochondrial DNA
genes
Mitochondrial Genome
Mutation Rate
Codon
mitochondrial DNA
rate
divergence
Melanogaster
codons
nuclear genome
Chemical analysis
methodology

Keywords

  • Drosophila
  • Mitochondria
  • Nuclear gene
  • Synonymous substitution rate
  • The melanogaster species subgroup
  • The obscura species group
  • Transition
  • Transversion

ASJC Scopus subject areas

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

Cite this

Synonymous substitution rates in Drosophila : Mitochondrial versus nuclear genes. / Moriyama, Etsuko N.; Powell, Jeffrey R.

In: Journal of Molecular Evolution, Vol. 45, No. 4, 16.10.1997, p. 378-391.

Research output: Contribution to journalArticle

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