Genomic analysis of Siphamia tubifer (Perciformes:Apogonidae) with ddRADseq

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 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. 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.