Molecular ecology of the Javanese ricefish, Oryzias javanicus (Bleeker): genetic divergence along the Indonesian Archipelago

Abstract

Context Investigating the patterns of genetic diversity and population structure of the Javanese ricefish, Oryzias javanicus, is instrumental in identifying their dispersal patterns and demographics in response to ecological changes and biogeographical barriers. Aims To acquire a better understanding of the evolutionary history of Javanese ricefish. Methods We sequenced part of the mitochondrial DNA (mtDNA) control region in 335 individuals and genotyped 280 individuals for four microsatellite loci from seven Indonesian sites. Key results Both genetic diversity (h = 0.19–0.86 and DIVGene = 0.10–0.43) and nucleotide diversity (π = 0.06–0.61%) were low compared with other fish taxa. The analysis of molecular variance showed considerable genetic differences (P < 0.0001) for both genetic markers across all sampled locations. These results suggest that there has been a historical restriction on gene flow. Conclusion The observed population-structure pattern reflects a short pelagic larval development, which is closely linked to a restricted dispersal potential. This ultimately leads to isolation by distance, potentially allowing local adaptation to sites that augment any oceanographic, geographic, or biological barriers to gene flow. Implications The results presented in this study can be used to create more effective ways to protect the species in question.