Abstract
Dams can landlock populations of amphidromous fishes that formerly migrated between rivers and seas. However, the genetic consequences of these life‐cycle changes remain unclear. Rhinogobius is a speciose genus of freshwater gobies widely distributed in Asia, including non‐migratory R. duospilus and facultatively amphidromous R. similis . Using genome‐wide SNPs from Hong Kong, southern China, we compared the genetic diversity and structure of R. duospilus (six populations), non‐landlocked R. similis (three populations), and landlocked R. similis (four populations) that had been isolated for 58–106 years. We also used demographic modelling to simulate patterns of gene flow of a panmictic amphidromous population of R. similis fragmented by dam construction 60 years ago. Rhinogobius duospilus populations were deeply divergent, with low genetic diversity; interpopulation differentiation reflected the underlying paleodrainage architecture. In contrast, non‐landlocked R. similis populations were genetically homogenous with high genetic diversity. However, all four landlocked populations of R. similis were highly differentiated, with three populations above tall (> 15 m) dams exhibiting comparable genetic clustering to non‐migratory R. duospilus , although overall genetic diversity remained high. Demographic modelling of a landlocked R. similis population indicated negligible migration into the reservoir and none outward, in accordance with the high levels of genetic divergence among landlocked populations. The effective population size of the original amphidromous population was small (Ne = 81), but the population landlocked above the reservoir for 60 years grew eightfold (Ne = 679). Our modelling suggests that even a limited level of immigration was sufficient to minimize genetic drift and lessen interpopulation divergence.