Data from: Genomic analysis of a cardinalfish with larval homing potential reveals genetic admixture in the Okinawa Islands

Discrepancies between potential and observed dispersal distances of reef fish indicate the need for a better understanding of the influence of larval behavior on recruitment and dispersal. Population genetic studies can reveal the degree to which populations are connected, providing insight on these patterns, and the development of restriction site associated sequencing (RAD-Seq) methods has made the study of non-model organisms more accessible. We applied double digest RAD-Seq methods to test for population differentiation in the coral reef-dwelling cardinalfish, Siphamia tubifer, which based on behavioral studies, have the potential to use navigational cues to return to natal reefs. Analysis of 11,836 SNPs from fish collected at coral reefs in Okinawa, Japan from eleven locations over three years reveal little genetic differentiation between groups of S. tubifer at spatial scales from 2 to 140 kilometers and between years at one location: pairwise FST values were 0.0116-0.0214. These results suggest that the Kuroshio Current largely influences larval dispersal in the region, and in contrast to expectations based on studies of other cardinalfishes, there is no evidence of population structure for S. tubifer at the spatial scales examined. However, analyses of outlier loci putatively under selection reveal patterns of temporal differentiation that indicate high population turnover and variable larval supply from divergent source populations. These findings highlight the need for more studies of fishes across various geographic regions that also examine temporal patterns of genetic differentiation to better understand the potential connections between early life history traits and connectivity of reef fish populations.