Extended Data Fig. 1: Gene order conservation.

a, Gene-order conservation score distribution using the tuatara as a reference. Species are ordered by the proportion of top-scoring orthologues ≥ 50. b, Gene-order conservation versus divergence time. For the three taxonomic groupings (Lepidosauria, Sauria and Amniota), we analysed the percentage of genes that are found in a conserved position across all pairs of genomes. Pairwise comparisons involving tuatara are shown in plain red circles (respectively, n = 8, n = 10, and n = 4), and comparisons that do not involve tuatara are black (box plot and + signs; respectively, n = 0, n = 80 and n = 72). The conservation of gene order between tuatara, birds and turtles is significantly higher (one-sided, two-sample Kolmogorov–Smirnov test, P value = 2.8 × 10⁻³, D = 0.575) than that observed between squamates, birds and turtles. As the tuatara is the only remaining rhynchocephalian, there is no control distribution for the Lepidosauria ancestor. Box plot coordinates (minimum, first quartile, median, mean, third quartile, maximum) are 42.46%, 57.93%, 66.00%, 64.50%, 70.66% and 84.76% for the Sauria box plot, and 21.52%, 40.81%, 57.43%, 55.17%, 69.46% and 82.34% for the Amniota box plot.