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Advances in next-generation sequencing technologies and the development of genome-reduced representation protocols have opened the way to genome-wide population studies in non-model species. However, species with large genomes remain challenging, hampering the development of genomic resources for a number of taxa including marine arthropods. Here, we developed a genome-reduced representation method for the ecologically important marine copepod  Calanus finmarchicus  (haploid genome size of 6.34 Gbp). We optimized a capture enrichment-based protocol based on 2656 single-copy genes, yielding a total of 154 087 high-quality SNPs in  C. finmarchicus  including 62 372 in common among the three locations tested. The set of capture probes was also successfully applied to the congeneric  C. glacialis . Preliminary analyses of these markers revealed similar levels of genetic diversity between the two  Calanus  species, while populations of  C. glacialis  showed stronger genetic structure compared to  C. finmarchicus . Using this powerful set of markers, we did not detect any evidence of hybridization between  C. finmarchicus  and  C. glacialis . Finally, we propose a shortened version of our protocol, offering a promising solution for population genomics studies in non-model species with large genomes.

Towards population genomics in non-model species with large genomes: a case study of the marine zooplanktonCalanus finmarchicus