Warm-blooded isochore structure in Nile crocodile and turtle

The genomes of warm-blooded vertebrates are characterized by a strong heterogeneity in base composition, with GC-rich and GC-poor isochores. The GC content of sequences, especially in third codon positions, is highly correlated with that of the isochore they are embedded in. In amphibian and fish genomes, GC-rich isochores are nearly absent. Thus, it has been proposed that the GC increase in a part of mammalian and avian genomes represents an adaptation to homeothermy. To test this selective hypothesis, we sequenced marker protein genes in two cold-blooded vertebrates, the Nile crocodile Crocodylus niloticus (10 genes) and the red-eared slider Trachemys scripta elegans (6 genes). The analysis of base composition in third codon position of this original data set shows that the Nile crocodile and the turtle also exhibit GC-rich isochores, which rules out the homeothermy hypothesis. Instead, we propose that the GC increase results from a mutational bias that took place earlier than the adaptation to homeothermy in birds and before the turtle/crocodile divergence. Surprisingly, the isochore structure appears very similar between the red-eared slider and the Nile crocodile than between the chicken and the Nile crocodile. This point questions the phylogenetic position of turtles as a basal lineage of extant reptiles. We also observed a regular molecular clock in the Archosauria, which enables us, by using a more extended data set, to confirm Kumar and Hedges's dating of the bird-crocodile split.