High evolutionary rates in nuclear genes of squamates

We compared nonsynonymous substitution rates (Ka) of nuclear coding genes b etween four major groups of living sauropsids (reptiles): birds, squamates, crocodiles, and turtles. Since only 9 orthologous genes are known in all t he four taxonomic groups, we searched for orthologous genes known in chicke n and at least one of any representative of poikilotherm sauropsids. Thus, we analyzed three additional data sets: 28 genes identified in chicken and various squamates, 24 genes identified in chicken and crocodilians, and 20 genes identified in chicken and turtles. To compare nonsynonymous substitut ion fates between all lineages of sauropsids, we used the relative-rate tes t with human genes as the outgroup. We show that 22/28 nuclear coding genes of squamates, especially snakes (15/16), have an higher evolutionary rate than those in chicken (in mean, 30-40% faster). However. no such difference is detected between crocodiles, turtles and chicken. Higher substitution r ate in squamates nuclear coding genes than in chicken, and probably than in other sauropsids, could explain some of the difficulties in resolving the molecular phylogeny of reptiles.