Table 1.

Comparison of alternative trees among Eulipotyphla (Eul), Chiroptera (Chi), Carnivora (Car), Cetartiodactyla (Cetart), and Perissodactyla (Per) with Euarchontoglires as an outgroup

Tree topology	10,666 sites (5)	16,671 sites (5)	Mitochondrial amino acids	Mitochondrial codons
1. (Eul,((Chi,(Per,Car)),Cetart))	〈−65,312.6〉	−3.0 ± 8.1	−23.8 ± 8.8	−23.4 ± 9.2
2. (Eul,(Chi,(Cetart,(Per,Car))))	−0.5 ± 2.2	−0.5 ± 6.8	〈−44,796.2〉	〈−118,056.2〉
3. (Eul,(Chi,((Cetart,Per),Car)))	−7.1 ± 6.4	〈−101,887.3〉	−3.2 ± 9.4	−3.5 ± 7.9
4. (Eul,((Chi,Cetart),(Per,Car)))	−0.6 ± 2.2	−3.2 ± 8.0	−16.1 ± 10.7	−12.8 ± 11.7
5. (Eul,((Chi,Car),(Cetart,Per)))	−4.3 ± 7.2	−0.6 ± 3.9	−20.7 ± 14.3	−25.5 ± 13.6
6. (Eul,((Chi,(Cetart,Car)),Per))	−8.6 ± 6.3	−8.1 ± 7.0	−26.7 ± 14.8	−29.3 ± 13.7
7. (Eul,((Chi,(Cetart,Per)),Car))	−6.2 ± 6.7	−1.3 ± 3.6	−24.4 ± 13.7	−25.9 ± 13.6
8. (Eul,(((Chi,Car),Cetart),Per))	−6.2 ± 6.9	−8.8 ± 7.2	−21.8 ± 15.6	−30.7 ± 14.1
9. (Eul,(((Chi,Cetart),Per),Car))	−7.7 ± 6.2	−9.2 ± 6.7	−21.8 ± 14.0	−19.5 ± 14.6
10. (Eul,((Chi,Per),(Cetart,Car)))	−6.6 ± 6.4	−2.4 ± 8.3	−35.2 ± 12.6	−33.3 ± 12.8
11. (Eul,(((Chi,Cetart),Car),Per))	−8.3 ± 6.2	−9.8 ± 7.1	−20.3 ± 15.1	−18.0 ± 15.0
12. (Eul,(((Chi,Car),Per),Cetart))	−4.8 ± 6.0	−7.9 ± 7.4	−30.7 ± 13.0	−35.0 ± 12.6
13. (Eul,(((Chi,Per),Car),Cetart))	−5.6 ± 5.8	−3.1 ± 8.7	−36.4 ± 12.1	−36.4 ± 12.3
14. (Eul,(((Chi,Per),Cetart),Car))	−5.6 ± 6.7	−3.3 ± 8.3	−32.4 ± 13.4	−34.5 ± 13.4
15. (Eul,(Chi,((Cetart,Car),Per)))	−9.1 ± 5.9	−6.2 ± 5.1	−10.8 ± 7.1	−8.1 ± 6.4

The log-likelihood of the ML tree is given in angled brackets, and the differences in the log-likelihoods of alternative trees from that of the ML tree ± 1 SE were estimated by using the formula of Kishino and Hasegawa (53). Comparison of trees other than the Eulipotyphla-basal in Laurasiatheria and P values of several tests are given in Tables 3–6, which are published as supporting information on the PNAS web site.