Fig. 1

Comparative framework to detect sequence divergence of regulatory elements in snakes. a Comparison of the tegu genome to genomes of other sequenced reptiles. N(x)% graph showing the contig and scaffold size (y-axis), where x% of the genome consists of contigs and scaffolds of at least that size. b Phylogenetic tree of the limbless and limbed species included in our multiple genome alignment. Snakes are in orange, remaining Episquamata species in green, remaining Sauropsida species in brown, and outgroup species in gray. All animal illustrations were taken from phylopic.org. c Overview of the computational steps to identify CNEs that are specifically diverged in snakes. d Filled gray and green density curves depict global and local Z-score distributions of 141,610 CNEs, respectively (22,812 CNEs with missing genomic sequence are excluded). Dashed curves depict the Z-score null distributions obtained by simulating the evolution of CNEs under selection in all amniote species