Insights into reproductive isolation within highly divergent copepod Pleuromamma abdominalis using genome-wide SNP data

Species complexes with multiple genetic clades are frequently observed using mitochondrial DNA (mtDNA) markers in pelagic copepods. However, reproductive isolation among clades is not fully understood because of low sequence variations in common nuclear markers. In the present study, genome-wide single nucleotide polymorphisms (SNPs) were obtained for copepod, Pleuromamma abdominalis, with the highly divergent and sympatric mtDNA clades using multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq). Sequences of mitochondrial cytochrome oxidase subunit I (mtCOI) were classified into six clades in 31 P. abdominalis that co-existed in the western subtropical North Pacific. Four mtCOI clades with genetic distances 0.082 were monophyletic according to the phylogenetic analyses based on SNPs in MIG-seq. Other two mtCOI clades with mean 0.082 genetic distance were not separated in MIG-seq analysis, and the results agreed with other genome-wide method of double digest restriction site associated DNA sequencing (ddRAD-seq). The genetic groups based on SNPs data were supported by the Bayesian clustering analysis, suggesting reproductive isolation and interbreeding among mtCOI clades. The two mtCOI clades with possible interbreeding have different distribution patterns, suggesting secondary contact without reproductive isolation in the sampling area. The genome-wide SNP data provided valuable insights into reproductive isolation of pelagic copepods. Thus, further studies using genome-wide methods, especially PCR-based approach including MIG-seq for small copepods, can lead to appropriate measurements of pelagic species diversity in the ocean.