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A phylogenomic study of human, dog, and mouse.

Cannarozzi G, Schneider A, Gonnet G - PLoS Comput. Biol. (2006)

Bottom Line: These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships.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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Computational Science, ETH Zurich, Zurich, Switzerland.

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.

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Rooted and Unrooted TopologiesUnrooted trees of three species (human, dog, mouse) display no information about the speciation order (center triplet). Only the use of an outgroup (opossum) places the root on one of the three branches (labeled A, B, and C), giving three possible rooted trees corresponding to the three hypotheses being tested.
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pcbi-0030002-g001: Rooted and Unrooted TopologiesUnrooted trees of three species (human, dog, mouse) display no information about the speciation order (center triplet). Only the use of an outgroup (opossum) places the root on one of the three branches (labeled A, B, and C), giving three possible rooted trees corresponding to the three hypotheses being tested.

Mentions: The evolutionary relationship of dog (Canis familiaris, order Carnivora), mouse (Mus musculus, order Rodentia), and human (Homo sapiens, order Primates) was examined applying a wide variety of distance measures and using the opossum (Monodelphis domestica) as the outgroup because, as a marsupial, it is the closest relative to the eutherian dataset. Thus, solving the problem of the phylogeny of the mouse, human, and dog requires finding the root of the tree. This can be achieved by placing the outgroup on one of the three branches leading to the orders. Figure 1 shows the three possible positions of the outgroup as well as the resulting rooted trees for the opossum and the three eutheria. We endeavored to answer the question of which of these three hypotheses—a primate–carnivore clade, a primate–rodent clade, or a rodent–carnivore clade—represents the true phylogeny.


A phylogenomic study of human, dog, and mouse.

Cannarozzi G, Schneider A, Gonnet G - PLoS Comput. Biol. (2006)

Rooted and Unrooted TopologiesUnrooted trees of three species (human, dog, mouse) display no information about the speciation order (center triplet). Only the use of an outgroup (opossum) places the root on one of the three branches (labeled A, B, and C), giving three possible rooted trees corresponding to the three hypotheses being tested.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1761043&req=5

pcbi-0030002-g001: Rooted and Unrooted TopologiesUnrooted trees of three species (human, dog, mouse) display no information about the speciation order (center triplet). Only the use of an outgroup (opossum) places the root on one of the three branches (labeled A, B, and C), giving three possible rooted trees corresponding to the three hypotheses being tested.
Mentions: The evolutionary relationship of dog (Canis familiaris, order Carnivora), mouse (Mus musculus, order Rodentia), and human (Homo sapiens, order Primates) was examined applying a wide variety of distance measures and using the opossum (Monodelphis domestica) as the outgroup because, as a marsupial, it is the closest relative to the eutherian dataset. Thus, solving the problem of the phylogeny of the mouse, human, and dog requires finding the root of the tree. This can be achieved by placing the outgroup on one of the three branches leading to the orders. Figure 1 shows the three possible positions of the outgroup as well as the resulting rooted trees for the opossum and the three eutheria. We endeavored to answer the question of which of these three hypotheses—a primate–carnivore clade, a primate–rodent clade, or a rodent–carnivore clade—represents the true phylogeny.

Bottom Line: These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships.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.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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Computational Science, ETH Zurich, Zurich, Switzerland.

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.

Show MeSH