Maximum likelihood estimate of vertebrate phylogeny (−ln likelihood = 239855.997). Likelihood analysis used the GTR + I + Γ model with parameter values estimated from the maximum parsimony tree. This model was significantly better by likelihood ratio test than the Tamura-Nei + I + Γ model (X ² = 15,792, d.f. = 3, P < 0.001). The tree shown had significantly greater likelihood for the present data than the generally accepted vertebrate tree, the maximum parsimony tree, and the LogDet distance tree indicated by the Shimodaira–Hasegawa (Shimodaira and Hasegawa 1999) test (P < 0.001 in each case). Scale bar indicates the probability of change per nucleotide site over the branch length interval shown. Lamprey was the designated outgroup.