A phylogenomic study of human, dog, and mouse

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.

Figure 1. Rooted and Unrooted Topologies

Unrooted 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.

Figure 2. Distance Phylogenetic Trees of Mammals

(A) The phylogenetic tree of the mammals is shown here with branch lengths obtained using different distance criteria shown in the tables: PAM distance (P), CodonPAM (CP), SynPAM (SP), and dS (dS). The branch lengths shown are proportional to PAM distance, and the circle indicates the placement of the root. (B) The phylogenetic tree of the mammals constructed using signed (S) and unsigned (U) reversal distance, with branch lengths proportional to the number of signed reversals.