a, The phylogeny topology of the nine teleosts was reconstructed with coalescent methods based on both orthologues and syntenic block datasets. The branch lengths represent divergence times, while the grey rectangle at each node indicates the 95% confidence interval. b, Demographic history estimated by PSMC. The three blue lines represent the three collected MHS individuals, while the green line represents Tanaka’s snailfish. c, Comparison of mutation rates in the nine sequenced fish species based on 4D sites. d, Mutation rates of three species, estimated by syntenic alignment along the stickleback genome. The numbers around the outside represent the chromosome ID of the stickleback genome. The blue, green and orange dots indicate the mutation rates for each window in the MHS, Tanaka’s snailfish and sticklebacks, respectively. The green and orange dots almost overlap, while the blue dots are appreciably closer to the centre of the figure (corresponding to a lower mutation rate across the genome). μ indicates the mutation rate (×10–9 site–1 yr–1) of each window. e–g, Two-dimension kernel density distribution of Ka (e), Ks (f) and Ka/Ks (that is, ω; g). The MHS has much lower Ks values but similar Ka values, and so has a much greater Ka/Ks ratio.