Insights into reproductive isolation within the pelagic copepod Pleuromamma abdominalis with high genetic diversity using genome-wide SNP data

Abstract

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 high genetic diversity 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. The other two mtCOI clades with mean 0.082 genetic distance were not separated in the MIG-seq phylogenetic tree. The results from our phylogenetic analysis of MIG-seq agreed with those from other genome-wide methods of double digest restriction site-associated DNA sequencing, and reproductive isolation and interbreeding between mtCOI clades were also supported by Bayesian clustering analysis. The two mtCOI clades that had possibly interbred exhibited different distribution patterns, suggesting secondary contact without reproductive isolation in the sampling area. The genome-wide SNP data supported the high cryptic species diversity in P. abdominalis, which was inferred from mitochondrial genes. Further genome-wide studies, especially those that use PCR-based approaches including MIG-seq for small copepods, can lead to appropriate measurements of pelagic species diversity in the ocean.