Supporting Information

Files in this Data Supplement:

Supporting Table 2
Supporting Figure 4
Supporting Figure 5
Supporting Figure 6
Supporting Table 3
Supporting Table 4
Supporting Table 5
Supporting Table 6
Supporting Figure 7
Supporting Table 7
Supporting Table 8
Supporting Table 9

Fig. 4. Alignments for seven loci that support the monophylies of Euarchontoglires (A), Glires (B), Laurasiatheria (C), Boreoeutheria (D), Scrotifera (E), Fereuungulata (F), and Zooamata (G). Thick and thin lines denote L1 sequences and direct repeat sequences, respectively, that were generated during integration. The central region of each inserted L1 sequence is omitted.

Fig. 5. The ML tree of 10,666 sites from the data of Murphy et al. [Murphy, W. J., Eizirik, E., O’Brien, S. J., Madsen, O., Scally, M., Douady, C. J., Teeling, E., Ryder, O. A., Stanhope, M. J., de Jong, W. W., et al. (2001) Science 294, 2348-2351], excluding indels and missing data sites. The clade Pegasoferae, which encompasses the orders Carnivora, Perissodactyla, and Chiroptera, is shown. The numbers on the branches indicate BPs.

Fig. 6. The ML tree of 16,671 sites from the data of Murphy et al. [Murphy, W. J., Eizirik, E., O’Brien, S. J., Madsen, O., Scally, M., Douady, C. J., Teeling, E., Ryder, O. A., Stanhope, M. J., de Jong, W. W., et al. (2001) Science 294, 2348-2351], including indels and missing data sites. The numbers on the branches indicate BPs.

Fig. 7. The ML tree of 12 protein-encoding gene sequences of mtDNA. The numbers on and below the branches indicate BPs analyzed at the amino acid and the codon level, respectively.