Phylogenetic relationships among eutherian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene |
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Authors: | Ying Cao Jun Adachi Axel Janke Svante Pääbo Masami Hasegawa |
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Affiliation: | (1) The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, 106 Minato-ku, Tokyo, Japan;(2) Department of Statistical Science, The Graduate University for Advanced Studies, 4-6-7 Minami-Azabu, 106 Minato-ku, Tokyo, Japan;(3) Department of Zoology, University of Munich, Luisenstrasse 14, D-8000 Munich 2, Germany |
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Abstract: | 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. |
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Keywords: | Opossum Outgroup Branching order Mammalian evolution Maximum likelihood tree |
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