Subregions of the study area defined for MIGRATE analysis.

1: South China Sea and Gulf of Thailand; 2: West Coast of Malay Peninsula; 3: West Java; 4: Celebes Sea and Flores Sea; 5: Guam; 6: Pacific Islands. Directionality of gene flows between selected subregions based on Cox3 is shown with Ne, the mean number of effective migrants per generation. All values are within the range of 440 to 665. Other details of gene flow among subregions based on all three markers are listed in Tables S6-S8 in File S1 respectively.