Global Rate Variation in Bony Vertebrates

This study investigated long-term substitution rate differences using three calibration points, divergences between lobe-finned vertebrates and ray-finned fish, between mammals and sauropsids, and between holosteans (gar and bowfin) and teleost fish with amino acid sequence data of 625 genes for 25 bony vertebrates. The result showed that the substitution rate was two to three times higher in the stem branches of lobe-finned vertebrates before the mammal-sauropsid divergence than in amniotes. The rate in the stem branch of ray-finned fish before the holostean-teleost fish divergence was also a few times higher than the holostean rate, whereas it was similar to or somewhat slower than the teleost fish rate. The phylogenetic relationship of coelacanth and lungfish with tetrapod was difficult to determine because of the short interval of the divergences. Considering the high rate in the stem branches, the divergences of coelacanth and lungfish from the stem branch were estimated as 408–427 Ma and 399–414 Ma, respectively, with the interval of 9–13 Myr. With the external calibration of the mammal-sauropsid split, the estimated times for ordinal divergences within eutherian mammals tend to be smaller than those in previous studies that used the calibration points within the lineage, with deeper divergences before the Cretaceous–Paleogene boundary and shallower ones after the boundary. In contrast the estimated times within birds were larger than those of previous studies, with the divergence between Galliformes and Anseriformes ∼80 Ma and that between Galloanserae and Neoaves 110 Ma.