Journal of Molecular Evolution

, Volume 39, Issue 5, pp 519–527

Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene


  • Ying Cao
    • The Institute of Statistical Mathematics
  • Jun Adachi
    • Department of Statistical ScienceThe Graduate University for Advanced Studies
  • Axel Janke
    • Department of ZoologyUniversity of Munich
  • Svante Pääbo
    • Department of ZoologyUniversity of Munich
  • Masami Hasegawa
    • The Institute of Statistical Mathematics
    • Department of Statistical ScienceThe Graduate University for Advanced Studies

DOI: 10.1007/BF00173421

Cite this article as:
Cao, Y., Adachi, J., Janke, A. et al. J Mol Evol (1994) 39: 519. doi:10.1007/BF00173421


The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall evidence of the maximum likelihood analysis suggests that Rodentia is an outgroup to the other four eutherian orders and that Cetacea and Artiodactyla form a clade with Carnivora as a sister taxon irrespective of the assumed model for amino acid substitutions. Although there remains an uncertainty concerning the relation among Artiodactyla, Cetacea, and Carnivora, the existence of a clade formed by these three orders and the outgroup status of Rodentia to the other eutherian orders seems to be firmly established. However, analyses of individual genes do not necessarily conform to this conclusion, and some of the genes reject the putatively correct tree with nearly 5% significance. Although this discrepancy can be due to convergent or parallel evolution in the specific genes, it was pointed out that, even without a particular reason, such a discrepancy can occur in 5% of the cases if the branching among the orders in question occurred within a short period. Due to uncertainty about the assumed model underlying the phylogenetic inference, this can occur even more frequently. This demonstrates the importance of analyzing enough sequences to avoid the danger of concluding an erroneous tree.

Key words

OpossumOutgroupBranching orderMammalian evolutionMaximum likelihood tree

Copyright information

© Springer-Verlag New York Inc 1994