Journal of Molecular Evolution

, Volume 53, Issue 2, pp 89–103

The Cytochrome b Gene as a Phylogenetic Marker: The Limits of Resolution for Analyzing Relationships Among Cichlid Fishes


  • Izeni P. Farias
    • Departamento de Biologia, Instituto de Ciências Biológicas, Universidade do Amazonas, 69077-000, Estrada do Contorno 3000, Manaus, Amazonas
  • Guillermo Ortí
    • School of Biological Sciences, 314 Manter Hall University of Nebraska, Lincoln, NE 68588-0118
  • Iracilda Sampaio
    • Laboratório de Biologia Molecular, Campus Universitário de Bragança Universidade Federal do Pará, Bragança, Pará
  • Horacio Schneider
    • Laboratório de Biologia Molecular, Campus Universitário de Bragança Universidade Federal do Pará, Bragança, Pará
  • Axel Meyer
    • Department of Biology, PO Box M617, University of Konstanz, D-78457 Konstanz

DOI: 10.1007/s002390010197

Cite this article as:
Farias, I., Ortí, G., Sampaio, I. et al. J Mol Evol (2001) 53: 89. doi:10.1007/s002390010197


The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total of 78 taxa were used in the present analysis, representing all the major groups in the family Cichlidae (72 taxa) and other families from the suborders Labroidei and Percoidei. Gene trees obtained from cyt-b are compared to a published total evidence tree derived from previous studies. Minimum evolution trees based on cyt-b data resulted in topologies congruent with all previous analyses. Parsimony analyses downweighting transitions relative to transversions (ts1:tv4) or excluding transitions at third codon positions resulted in more robust bootstrap support for recognized clades than unweighted parsimony. Relative rate tests detected significantly long branches for some taxa (LB taxa) which were composed mainly by dwarf Neotropical cichlids. An improvement of the phylogenetic signal, as shown by the four-cluster likelihood mapping analysis, and higher bootstrap values were obtained by excluding LB taxa. Despite some limitations of cyt-b as a phylogenetic marker, this gene either alone or in combination with other data sets yields a tree that is in agreement with the well-established phylogeny of cichlid fish.

Key words: Cichlid fishes — Phylogeny — Cytochrome b— Systematics — Long branches — DNA substitution rate

Copyright information

© Springer-Verlag New York Inc. 2001