A Phylogenomic Study of Human, Dog, and Mouse

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Abstract
In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria—distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate–carnivore clade with the exclusion of rodents. Some basal relationships in the eutherian tree have been difficult to resolve, probably because the underlying divergences took place within a very short period of time. In this study we examine particularly the relationship between human (primates), dog (carnivores), and mouse (rodents). Previous morphological and molecular studies using different datasets and reconstruction methods have come to different conclusions about the relative placement of these orders on the mammalian tree. Here, we use completely sequenced nuclear genomes and a number of different phylogenetic methods to address this difficult problem. An approach of this kind has only recently become possible with the sequencing of several complete mammalian genomes including the opossum as a relevant outgroup. Our results strongly suggest a sister relationship between primates and carnivores.