Cryptic population substructure in Cape Hakes

<p>Genomic information has the potential to aid in the establishment of sustainable management plans for commercially exploited marine fishes, aiding in the long-term conservation of these resources. The southern African hakes (<em>Merluccius</em> <em>capensis</em> and <em>M</em>. <em>paradoxus</em>) are commercially valuable demersal fishes with similar distribution ranges but exhibiting contrasting life histories. Using a comparative framework based on Pool-Seq genome-wide SNP data, we investigated <span>whether the evolutionary processes that shaped </span>extant patterns of diversity and divergence are shared among these two congeneric fishes, or unique to each one. Our findings revealed that <em>M. capensis </em>and<em> M. paradoxus</em> show similar levels of genome-wide diversity, despite different census sizes and life-history features. In addition, <em>M. capensis</em> shows three highly structured geographic populations across the Benguela Current region (one in the northern Benguela and two in the southern Benguela), with no consistent genome-environment associations detected. In contrast, although population structure and outlier analyses suggested panmixia for <em>M. paradoxus</em>, reconstruction of its demographic history suggested the presence of an Atlantic-Indian Ocean subtle sub-structuring pattern. Therefore, it appears that <em>M. paradoxus</em> might be composed of two highly connected populations, one in the Atlantic and one in the southwest Indian Ocean. The reported similarly low levels of genomic diversity, as well as newly discovered genetically distinct populations in both hake species can thus assist in informing and improving conservation and management plans for the commercially important southern African <em>Merluccius</em>.</p>