Journal of Molecular Evolution

, 66:232

A Candidate Complex Approach to Study Functional Mitochondrial DNA Changes: Sequence Variation and Quaternary Structure Modeling of Drosophila simulans Cytochrome c Oxidase

  • Richard G. Melvin
  • Subhash D. Katewa
  • J. William O. Ballard
Article

DOI: 10.1007/s00239-008-9078-4

Cite this article as:
Melvin, R.G., Katewa, S.D. & Ballard, J.W.O. J Mol Evol (2008) 66: 232. doi:10.1007/s00239-008-9078-4

Abstract

A problem with studying evolutionary dynamics of mitochondrial (mt) DNA is that classical population genetic techniques cannot identify selected substitutions because of genetic hitchhiking. We circumvented this problem by employing a candidate complex approach to study sequence variation in cytochrome c oxidase (COX) genes within and among three distinct Drosophila simulans mtDNA haplogroups. First, we determined sequence variation in complete coding regions for all COX mtDNA and nuclear loci and their isoforms. Second, we constructed a quaternary structure model of D. simulans COX. Third, we predicted that six of nine amino acid changes in D. simulans mtDNA are likely to be functionally important. Of these seven, genetic crosses can experimentally determine the functional significance of three. Fourth, we identified two single amino acid changes and a deletion of two consecutive amino acids in nuclear encoded COX loci that are likely to influence cytochrome c oxidase activity. These data show that linking population genetics and quaternary structure modeling can lead to functional predictions of specific mtDNA amino acid mutations and validate the candidate complex approach.

Keywords

Genetic hitchhikingCytochrome c oxidaseCandidate complex approach

Supplementary material

239_2008_9078_MOESM1_ESM.doc (770 kb)
MOESM 1 (DOC 770 kb)

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Richard G. Melvin
    • 1
  • Subhash D. Katewa
    • 1
  • J. William O. Ballard
    • 1
  1. 1.Ramaciotti Centre for Gene Function Analysis, School of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyAustralia