Population genomics reveals dispersal barriers in the subtropical shelled pteropod Limacina bulimoides

Pteropods are regarded as potential bio-indicators of the changing ocean environment because of their thin aragonitic shell, which is susceptible to dissolution. To gain insight into their capacity for evolutionary responses to ocean change, we require knowledge on the level of genetic variability and degree of population connectivity within species. Little is known about population genetic structures in pteropods, in part due to a lack of genomic resources, because of their potentially large genomes and small body sizes. We chose a population genomic approach and used a genome-reduced representation protocol of capture enrichment to investigate dispersal barriers in 8 groups of individuals (7 from the Atlantic and 1 from the Pacific Ocean) of the shelled pteropod species Limacina bulimoides. A set of 2,900 genome-wide probes was designed for this species, including 2,812 single copy nuclear targets, the 28S rDNA sequence, 10 known mitochondrial genes, 35 candidate biomineralisation genes, and 42 non-coding regions. Based on the ~95,000 single nucleotide polymorphism (SNP) markers detected across 80 individuals, we found three genetically distinct populations in the Atlantic Ocean: one associated with the North Atlantic Subtropical Gyre and the other two populations with the South Atlantic Subtropical Gyre. The strongest divergence was detected between the Atlantic and Pacific populations, suggesting an ancient barrier to gene flow. These two groups may even represent distinct species. Finally, the genome-wide SNP panel developed in this study allows for analyses of historical demography and association with environmental variables, shedding further light on the evolutionary potential of pteropods.