Fig. 3: Analysis of sex differences, demographic history and population structure.

a, Methylation levels in the tuatara genome are high (mean 81%), but show no significant differences among the sexes (female n = 13, mean = 81.13, s.d. = 1.55; male n = 12; mean = 81.02, s.d.−1.07). The black horizontal line represents the mean in each dataset. b, No single-nucleotide variant (SNV) is significantly differentiated with respect to sex in the tuatara genome. Each point represents a P value from a test of sexual differentiation for a single SNV. The dashed line represents the threshold for statistical significance after accounting for multiple testing (n = 28; 13 males and 15 females). P values calculated using Fisher’s exact test, two-tailed test and corrected for multiple testing using the Bonferroni method. c, Pairwise sequential Markovian coalescent plot of the demographic history of tuatara using a mutation rate of 1.4 × 10⁻⁸ substitutions per site per generation and a generation time of 30 years. d, We examined the three known axes of genetic diversity in tuatara: northern New Zealand (Little Barrier Island (LBI) (n = 9)) and two islands in the Cook Strait (Stephens Island (SI) (n = 9) and North Brother Island (NBI) (n = 10)), using genotype-by-sequencing methods. Principal component (PC) analysis and structure plots demonstrate substantial structure among tuatara populations, and strongly support previous suggestions that the tuatara on the North Brother Island are genetically distinct and warrant separate management.