Detection of gene flow between subspecies
We used the statistical model implemented in TreeMix to infer patterns of splits and mixtures among populations (Pickrell & Pritchard, 2012). As revealed from the FST statistic above, some populations are genetically similar, e.g. Andaman Sea on the west of Malay Peninsula and the South China Sea (Gulf of Thailand and Hainan Island). Hence, one representative population from each region was used in this analysis. The twelve populations were related to the common ancestor through a graph of ancestral populations, which was inferred by allele frequency and a Gaussian approximation to genetic drift (Pickrell & Pritchard, 2012). Gene flow events were inferred by adding admixtures onto the Maximum Likelihood population splitting topology.