Marine Biotechnology

, Volume 6, Issue 6, pp 516–526 | Cite as

Variation in Coding (NADH Dehydrogenase Subunits 2, 3, and 6) and Noncoding Intergenic Spacer Regions of the Mitochondrial Genome in Octocorallia (Cnidaria: Anthozoa)

  • Catherine S. McFaddenEmail author
  • Ian D. Tullis
  • M. Breton Hutchinson
  • Katherine Winner
  • Jill A. Sohm


Low rates of evolution in cnidarian mitochondrial genes such as COI and 16S rDNA have hindered molecular systematic studies in this important invertebrate group. We sequenced fragments of 3 mitochondrial protein-coding genes (NADH dehydrogenase subunits ND2, ND3 and ND6) as well as the COI-COII intergenic spacer, the longest noncoding region found in the octocoral mitochondrial genome, to determine if any of these regions contain levels of variation sufficient for reconstruction of phylogenetic relationships among genera of the anthozoan subclass Octocorallia. Within and between the soft coral families Alcyoniidae and Xeniidae, sequence divergence in the genes ND2 (539 bp), ND3 (102 bp), and ND6 (444 bp) ranged from 0.5% to 12%, with the greatest pairwise distances between the 2 families. The COI-COII intergenic spacer varied in length from 106 to 122 bp, and pairwise sequence divergence values ranged from 0% to 20.4%. Phylogenetic trees constructed using each region separately were poorly resolved. Better phylogenetic resolution was obtained in a combined analysis using all 3 protein-coding regions (1085 bp total). Although relationships among some pairs of species and genera were well supported in the combined analysis, the base of the alcyoniid family tree remained an unresolved polytomy. We conclude that variation in the NADH subunit coding regions is adequate to resolve phylogenetic relationships among families and some genera of Octocorallia, but insufficient for most species - or population-level studies. Although the COI-COII intergenic spacer exhibits greater variability than the protein-coding regions and may contain useful species-specific markers, its short length limits its phylogenetic utility.


Alcyoniidae mitochondrial DNA ND2 ND3 ND6 octocoral phylogenetics 



We thank John Starmer for providing and identifying many of the specimens used, Andrew Schile for primer design, Nicholas Johnson for assistance with data analysis, Michael McMillin of the Rancho Santa Ana Botanic Garden for DNA sequencing, and Juan Sánchez and one anonymous reviewer for comments on the manuscript. This study was supported by a Beckman Faculty Research Award and grants to the Harvey Mudd College Biology Department from the Frank M. Parsons Foundation and the Arthur Vining Davis Foundation. Support for I.D. Tullis and M.B. Hutchinson was provided by Munzer and Emily Mudd Summer Research Fellowships.


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Copyright information

© Springer Science+Business Media, Inc. 2004

Authors and Affiliations

  • Catherine S. McFadden
    • 1
    Email author
  • Ian D. Tullis
    • 1
    • 2
  • M. Breton Hutchinson
    • 1
    • 3
  • Katherine Winner
    • 1
  • Jill A. Sohm
    • 1
    • 4
  1. 1.Department of BiologyHarvey Mudd CollegeClaremontU.S.A.
  2. 2.Present address: Ecosystem Sciences Division, Department of Environmental Science, Policy and Management, University of California BerkeleyU.S.A.
  3. 3.Present address: Department of Molecular and Cell Biology, University of California, BerkeleyU.S.A.
  4. 4.Present address: Wrigley Institute for Environmental Studies, Department of Biological Sciences, University of Southern California Los AngelesU.S.A.

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