Extended Data Fig. 9: Estimated DNA substitution rates of amniote clades on the basis of fourfold-degenerate sites and a test for evidence of punctuated evolution.

a, Box plots showing distribution of estimated substitution rates by clade using semiparametric penalized likelihood in r8s with fossil constraints from ref. ³⁶ and ref. ³⁷ for tuatara (n = 1, 0.00159), squamates (n = 13, minimum = 0.00171, maximum = 0.00183, median = 0.00178, 25th percentile = 0.00178, 75th percentile = 0.00183), turtles (n = 3, minimum = 0.00138, maximum = 0.00141, median = 0.00140, 25th percentile = 0.00139, 75th percentile = 0.00140), crocodilians (n = 5, minimum = 0.00128, maximum = 0.0133, median = 0.00129, 25th percentile = 0.00129, 75th percentile = 0.00129), birds (n = 11, minimum = 0.0014, maximum = 0.00152, median = 0.00147, 25th percentile = 0.00146, 75th percentile = 0.0015) and mammals (n = 15, minimum = 0.00188, maximum = 0.00208, median = 0.00197, 25th percentile = 0.00194, 75th percentile = 0.00201). b, Box plots showing distribution of estimated substitution rates with median time to most recent common ancestor estimates from www.timetree.org for tuatara (n = 1, 0.00157), squamates (n = 13, minimum = 0.00168, maximum = 0.00180, median = 0.00175, 25th percentile = 0.00178, 75th percentile = 0.00177), turtles (n = 3, minimum = 0.00138, maximum = 0.00141, median = 0.00140, 25th percentile = 0.00139, 75th percentile = 0.00140), crocodilians (n = 5, minimum = 0.00129, maximum = 0.0134, median = 0.00130, 25th percentile = 0.00130, 75th percentile = 0.00130), birds (n = 11, minimum = 0.00142, maximum = 0.00154, median = 0.00149, 25th percentile = 0.00147, 75th percentile = 0.00152) and mammals (n = 15, minimum = 0.00188, maximum = 0.00206, median = 0.00197, 25th percentile = 0.00194, 75th percentile = 0.00199). c, A test for evidence of punctuated evolution. The process of punctuated genome evolution predicts that the amount of evolution in the genome of a given species should correlate with the net number of speciation events. We used Bayesian phylogenetic generalized least squares to regress the total phylogenetic path length (of fourfold-degenerate sites) on the net number of speciation events (nodes in a phylogenetic tree). We find strong evidence for punctuated evolution, which accounts for 33.5% (r²; 95% credible interval = 0.34 to 0.38) of deviation from the molecular clock at fourfold-degenerate sites.