Geographical barrier identification and test of isolation by distance
By calculating Monmonier’s maximum difference using the program BARRIER, we inferred four strong geographic barriers. The robustness of each barrier was assessed by bootstrapping over 100 matrices ofFST , with each matrix calculated from 30 genes randomly sampled from the 93 sequenced genes. The first barrier, supported by the 99 FST matrix, aligns with the Malay Peninsula, isolating La-un and Nago from Chai-ya (Figure 5a). The second barrier, with the support of 85 matrices, lies in the Indonesian archipelago, isolated Bali from Kuching (Figure 5a). Both of the two barriers are part of the Sundaland barrier. The third barrier lies in the Wallacea region, supported with 93,75 and 75 matrices (Figure 5a). This barrier isolated the populations in Australasia from those in Southeast Asia. The fourth barrier, which is supported by 95, 95, and 59 matrices, lies between the northern South China Sea and southern South China Sea (Figure 5a).
The Mantel test revealed a significant correlation (r =0.518, P<0.01) between geographical distance and genetic differentiation of Sanger FST estimations (Figure 5b). The same test using Solexa data also showed a significant correlation (r=0.485, P-value < 0.01, Figure S7). The Mantel tests within the “Pan-Australasia” group (r=0.560, P-value <0.01, Figure S8) and “Indo-Malayan” group (r=0.698, P-value <0.01, Figure S9) showed even more stronger correlations. This indicated isolation by distance had contributed to the population differentiation. Despite the significant r-value, the population structures revealed before were evidenced by that the population pairs within subgroups showed much smaller FST values than the IBD expectation while the population pairs of s-SCS vs. n-SCS or s-SCS vs. the Indian Ocean showed much largerFST (Figure 5b).