Thermal heterogeneity is an important factor for maintaining the genetic differentiation pattern of the pelagic barnacle in the northwest Pacific.

Macrobenthic invertebrates are ubiquitously distributed in the epipelagic zone of the open ocean. Yet, our understanding of their genetic structure patterns remains poorly understood. Investigating the genetic differentiation patterns of pelagic and clarifying the potential roles of temperature maintaining this pattern are crucial for our understanding of the distribution and biodiversity of pelagic macrobenthos. In the present study, mitochondrial cytochrome oxidase subunit I (mtDNA COI) from three South China Sea (SCS) populations and six Kuroshio Extension (KE) region populations of sampled from fixed buoys and genome-wide SNPs from a subset of populations (two SCS populations and four KE region populations) were sequenced and analyzed for investigating the genetic pattern of the pelagic barnacle. Water temperature was different among sampling sites; in other words, the water temperature decreased with latitude increases, and the water temperature on the surface was higher than in the subsurface. Our result showed that three lineages with clear genetic differentiation were found in different geographical locations and depths based on mtDNA COI, all SNPs, neutral SNPs, and outlier SNPs. Lineage 1 and lineage 2 were dominant in the subsurface populations and surface populations from the KE region, respectively. Lineage 3 was dominant in the SCS populations. Historical events during the Pliocene epoch shaped the differentiation of the three lineages, while, nowadays, temperature heterogeneity maintains the current genetic pattern of in the northwest Pacific. The subsurface populations were genetically isolated from the surface populations in the Kuroshio Extension (KE) region, implying small-scale vertical thermal heterogeneity was also an important factor maintaining the genetic differentiation pattern of the pelagic species.